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source: palm/trunk/SCRIPTS/palmrun @ 2512

Last change on this file since 2512 was 2512, checked in by raasch, 7 years ago

upper bounds of cross section and 3d output changed from nx+1,ny+1 to nx,ny; no output if redundant ghost layer data to NetCDF files
  • Property svn:executable set to *
  • Property svn:keywords set to Id
File size: 86.0 KB
Line 
1#!/bin/bash
2
3# palmrun - script for running PALM jobs
4
5#--------------------------------------------------------------------------------#
6# This file is part of PALM.
7#
8# PALM is free software: you can redistribute it and/or modify it under the terms
9# of the GNU General Public License as published by the Free Software Foundation,
10# either version 3 of the License, or (at your option) any later version.
11#
12# PALM is distributed in the hope that it will be useful, but WITHOUT ANY
13# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
14# A PARTICULAR PURPOSE.  See the GNU General Public License for more details.
15#
16# You should have received a copy of the GNU General Public License along with
17# PALM. If not, see <http://www.gnu.org/licenses/>.
18#
19# Copyright 2017  Leibniz Universitaet Hannover
20#--------------------------------------------------------------------------------#
21#
22# Current revisions:
23# ------------------
24#
25#
26# Former revisions:
27# -----------------
28# $Id: palmrun 2512 2017-10-04 08:26:59Z raasch $
29# bugfix for determining cycle numbers of NetCDF input files
30#
31# 2506 2017-09-29 08:30:37Z raasch
32# option -V added to check for an existing SOURCES_FOR_RUN_... folder
33# host configuration added to SOURCES_FOR_RUN_... folder name
34# host_identifier renamed host_configuration
35# option -W added to allow for job dependencies
36#
37# 2501 2017-09-26 11:41:55Z raasch
38# default value for number of cores (option -X) set to 1
39# bugfix for mechanism which overwrites configuration file settings with values
40# provided by palmrun options
41#
42# 2499 2017-09-22 16:47:58Z kanani
43# option -h named configuration identifier
44#
45# 2480 2017-09-19 06:24:14Z maronga
46# bugfix for last revision
47#
48# 2479 2017-09-19 06:12:16Z raasch
49# option -A (project account number) added
50#
51# 2422 2017-09-08 08:25:41Z raasch
52# initial revision
53#
54#--------------------------------------------------------------------------------#
55# palmrun - script for running PALM jobs on local and remote hosts
56#--------------------------------------------------------------------------------#
57
58
59 
60    # DECLARATION OF VARIABLES AND THEIR DEFAULT VALUES
61
62 set +o allexport    # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
63                     # LEAD TO PROBLEMS IN ROUTINES CALLED BY PALMRUN
64                     # (TOO MANY ARGUMENTS - PROBLEM)
65 set +o noclobber    # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
66
67 typeset -i  ibd=0 ibdt=0 iec=0 iic=0 iin=0 ioc=0 iout=0
68 typeset -x -i  memory=0   # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
69                           # SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
70                           # SCRIPT-OPTION ARGUMENTS
71 typeset -i  cores cputime cpu_hours cpu_minutes cpu_seconds i ii iia iii iio
72 typeset -i  icycle inode ival maxcycle mpi_tasks
73 typeset -i  nodes remaining_cores run_number tasks_per_node threads_per_task
74
75 activation_string_list=""
76 AddFilenames=""
77 combine_plot_fields=true
78 compiler_name=""
79 compiler_name_ser=""
80 compiler_options=""
81 cores=1
82 cores_atmos=0
83 cores_ocean=0
84 coupled_dist=""
85 cpp_options=""
86 cpumax=0
87 create_batch_job=false
88 create_jobfile_only=false
89 create_remote_batch_job=false
90 dashes="  ----------------------------------------------------------------------------"
91 defaultqueue=""
92 delete_temporary_catalog=true
93 do_compile=true
94 do_trace=false
95 executable=""
96 execute_command=""
97 execution_error=false
98 fileconnection_file=.palm.iofiles
99 fname=test
100 global_revision=""
101 host_configuration="default"
102 hostfile=""
103 hp=""
104 keep_data_from_previous_run=false
105 link_local_input=false
106 link_local_output=false
107 linker_options=""
108 local_jobcatalog=""
109 locat=normal
110 makefile=""
111 max_par_io_str=""
112 prc=$0
113 while [[ $(echo $prc | grep -c "/") != 0 ]]
114 do
115    prc=`echo $prc | cut -f2- -d"/"`
116 done
117 module_calls=""
118 palmrun_memory=""
119 palmrun_script_name=$prc
120 openmp=false
121 previous_job=""
122 project_account=""
123 queue=none
124 restart_run=false
125 return_address=""
126 remote_jobcatalog=""
127 remote_username=""
128 running_in_batch_mode=false
129 run_coupled_model=false
130 run_id=""
131 silent=false
132 source_list=""
133 source_path=""
134 tasks_per_node=0
135 threads_per_task=1
136 tmpcreate=false
137 transfer_problems=false
138 user_source_path=""
139 use_existing_sources_folder=""
140 use_openmp=false
141 version="palmrun  1.0 Rev$Rev: 2303 $"
142 working_directory=`pwd`
143 write_binary=""
144 TOPT=""
145
146
147    # ERROR HANDLING IN CASE OF EXIT
148 trap 'if [[ $locat != normal  &&  $locat != control_c ]]
149       then
150
151              # CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
152          (( i = 0 ))
153          while (( i < iec ))
154          do
155             (( i = i + 1 ))
156             printf "\n  *** Execution of ERROR-command:\n"
157             printf "  >>> ${err_command[$i]}\n"
158             eval  ${err_command[$i]}
159          done
160          [[ $delete_temporary_catalog = true ]]  &&  (cd; rm -rf $TEMPDIR)
161          printf "\n\n+++ palmrun killed \n\n"
162       elif [[ $locat != control_c ]]
163       then
164          printf "\n\n --> palmrun finished\n\n"
165          if [[ $running_on_remote = true ]]
166          then
167             printf "     Bye, bye $remote_username !!\n\n"
168          else
169             printf "     Bye, bye $local_username !!\n\n"
170          fi
171       fi' exit
172
173
174    # ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
175 trap 'cd; rm -rf $TEMPDIR
176       printf "\n+++ palmrun killed by \"^C\" \n\n"
177       locat=control_c
178       exit
179      ' 2
180
181
182    # READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc),
183    # WHICH WILL BE USED TO START RESTART-JOBS
184 while  getopts  :a:A:bBCd:FG:h:jkm:M:O:q:r:R:s:t:T:u:U:vVw:W:xX:yY:Z option
185 do
186   case  $option  in
187       (a)   activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";;
188       (A)   project_account=$OPTARG; prc="$prc -A'$OPTARG'";;
189       (b)   create_batch_job=true; prc="$prc -b";;
190       (B)   delete_temporary_catalog=false; prc="$prc -B";;
191       (C)   restart_run=true; prc="$prc -C";;
192       (d)   fname=$OPTARG; prc="$prc -d$OPTARG";;
193       (F)   create_jobfile_only=true;;
194       (G)   global_revision=$OPTARG; prc="$prc -G'$OPTARG'";;
195       (h)   host_configuration=$OPTARG; prc="$prc -h$OPTARG";;
196       (j)   running_in_batch_mode=true;;
197       (k)   keep_data_from_previous_run=true; prc="$prc -k";;
198       (m)   palmrun_memory=$OPTARG; prc="$prc -m$OPTARG";;
199       (M)   makefile=$OPTARG; prc="$prc -M$OPTARG";;
200       (O)   use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";;
201       (q)   queue=$OPTARG; prc="$prc -q$OPTARG";;
202       (r)   run_id=$OPTARG;;
203       (R)   return_address=$OPTARG;;
204       (s)   source_list=$OPTARG;;
205       (t)   palmrun_cpumax=$OPTARG; prc="$prc -t$OPTARG";;
206       (T)   palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";;
207       (u)   remote_username=$OPTARG; prc="$prc -u$OPTARG";;
208       (U)   return_username=$OPTARG; prc="$prc -U$OPTARG";;
209       (v)   silent=true; prc="$prc -v";;
210       (V)   use_existing_sources_folder="-V";;
211       (w)   max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";;
212       (W)   previous_job=$OPTARG;;
213       (x)   do_trace=true;set -x; prc="$prc -x";;
214       (X)   palmrun_cores=$OPTARG; prc="$prc -X$OPTARG";;
215       (y)   ocean_file_appendix=true; prc="$prc -y";;
216       (Y)   run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";;
217       (Z)   combine_plot_fields=false; prc="$prc -Z";;
218       (\?)  printf "\n  +++ unknown option $OPTARG \n"
219             printf "\n  --> type \"$0 ?\" for available options \n"
220             locat=parameter;exit;;
221   esac
222 done
223
224
225    # SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
226    # CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
227 (( to_shift = $OPTIND - 1 ))
228 shift $to_shift
229
230    # PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS
231 if [[ "$1" = "?" ]]
232 then
233   (printf "\n  *** Description of available palmrun options:\n"
234    printf "\n      Option  Description                              Default-Value"
235    printf "\n        -a    activation string list                   \"\" "
236    printf "\n        -A    project account number                   ---"
237    printf "\n        -b    batch-job on local machine               ---"
238    printf "\n        -B    do not delete temporary directory at end ---"
239    printf "\n        -d    base name of files attached to program   test"
240    printf "\n        -F    create batch job file only               ---"
241    printf "\n        -h    host configuration                       \"default\" "
242    printf "\n        -k    keep data from previous run"
243    printf "\n        -m    memory demand in MB (batch-jobs)         0 MB"
244    printf "\n        -M    Makefile name                            Makefile"
245    printf "\n        -O    threads per openMP task                  ---"
246    printf "\n        -q    queue                                    \"$queue\" "
247    printf "\n        -s    filenames of routines to be compiled     \"\" "
248    printf "\n              must end with .f, .f90, .F, or .c !"
249    printf "\n              use \"..\" for more than one file and wildcards"
250    printf "\n              -s LM compiles all locally modified files"
251    printf "\n        -t    allowed cpu-time in seconds (batch)      0"
252    printf "\n        -T    tasks per node                           ---"
253    printf "\n        -u    username on remote machine               \"\" "
254    printf "\n        -v    no prompt for confirmation               ---"
255    printf "\n        -V    check if SOURCES_FOR_RUN_... exists      ---"
256    printf "\n        -w    maximum parallel io streams              as given by -X"
257    printf "\n        -W    name of job to wait for                  ---"
258    printf "\n        -x    tracing of palmrun for debug purposes    ---"
259    printf "\n        -X    # of processors (on parallel machines)   1"
260    printf "\n        -y    add appendix \"_O\" to all local output"
261    printf "\n              files (ocean precursor runs followed by"
262    printf "\n              coupled atmosphere-ocean runs)           ---"
263    printf "\n        -Y    run coupled model, \"#1 #2\" with" 
264    printf "\n              #1 atmosphere and #2 ocean processors    \"#/2 #/2\" depending on -X"
265    printf "\n        -Z    skip combine_plot_fields at the end of      "
266    printf "\n              the simulation                           ---"
267    printf "\n "
268    printf "\n      Possible values of positional parameter <modus>:"
269    printf "\n        \"?\"       -  this outline \n\n") | more
270    exit
271 elif [[ "$1" != "" ]]
272 then
273    printf "\n  +++ positional parameter $1 unknown \n"
274    locat=parameter; exit
275 fi
276
277
278
279    # SHORT STARTING MESSAGE
280 printf "\n*** $version "
281 printf "\n    will be executed.     Please wait ..."
282
283
284    # BUILD THE CONFIGURATION-FILE NAME AND THE SOURCES_FOR_RUN-FOLDER NAME
285 config_file=.palm.config.$host_configuration
286 sources_for_run_catalog=SOURCES_FOR_RUN_${host_configuration}_$fname
287
288
289    # CHECK, IF CONFIGURATION FILE EXISTS
290 if [[ ! -f $config_file ]]
291 then
292    printf "\n\n  +++ configuration file: "
293    printf "\n           $config_file"
294    printf "\n      does not exist"
295    locat=connect; exit 
296 fi
297
298
299    # CHECK, IF FILE CONNECTION FILE EXISTS
300 if [[ ! -f $fileconnection_file ]]
301 then
302    printf "\n\n  +++ file connection file: "
303    printf "\n           $fileconnection_file"
304    printf "\n      does not exist"
305    locat=connect; exit 
306 fi
307
308
309    # CHECK, IF THE ACTIVATION_STRING_LIST HAS BEEN GIVEN
310 if [[ "$activation_string_list" = "" ]]
311 then
312    printf "\n\n  +++ no activation string list given: "
313    printf "\n        please set palmrun option \"-a\" "
314    locat=palmrun_option; exit 
315 fi
316
317
318    # SET VARIABLE TO ACTIVATE PALM BINARY OUTPUT FOR RESTARTS
319 if [[ $(echo $activation_string_list | grep -c "restart") != 0 ]]
320 then
321    write_binary=true
322 else
323    write_binary=false
324 fi
325
326
327    # READ AND EVALUATE THE CONFIGURATION-FILE
328 [[ $silent = false ]]  &&  printf "\n\n    Reading the configuration file... "
329
330    # READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE
331 while  read line
332 do
333
334       # FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
335    eval  line=\"$line\"
336
337
338       # INTERPRET THE LINE
339    if [[ "$(echo $line)" = "" ]]
340    then
341
342          # EMPTY LINE, NO ACTION
343       continue
344
345    elif [[ "$(echo $line | cut -c1)"  =  "#" ]]
346    then
347
348          # LINE IS A COMMENT LINE
349       continue
350
351    elif [[ "$(echo $line | cut -c1)"  =  "%" ]]
352    then
353
354          # LINE DEFINES AN ENVIRONMENT-VARIABLE
355       var=`echo $line | cut -d" " -s -f1 | cut -c2-`
356       value=`echo $line | cut -d" " -s -f2-`
357
358
359          # VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
360          # ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
361          # ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
362          # NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
363          # HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
364          # CONFIGURATION-FILE.
365       if [[ "$(eval echo \$$var)" = ""  ||  "$(eval echo \$$var)" = "0" ]]
366       then
367          eval  export  $var="\$value"
368
369             # TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
370          if [[ $do_trace = true ]]
371          then
372             printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
373          fi
374       fi
375
376    elif [[ "$(echo $line | cut -c1-3)" = "BD:" ]]
377    then
378
379          # LINE DEFINES BATCH-DIRECTIVE
380       (( ibd = ibd + 1 ))
381       line=$(echo $line | cut -c4-)
382       batch_directive[$ibd]="$line"
383
384    elif [[ "$(echo $line | cut -c1-4)" = "BDT:" ]]
385    then
386
387          # LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A
388          # REMOTE TO A LOCAL HOST
389       (( ibdt = ibdt + 1 ))
390       line=$(echo $line | cut -c5-)
391       batch_directive_transfer[$ibdt]="$line"
392
393    elif [[ "$(echo $line | cut -c1-3)" = "EC:" ]]
394    then
395
396          # LINE DEFINES ERROR-COMMAND
397       (( iec = iec + 1 ))
398       line=$(echo $line | cut -c4-)
399       err_command[$iec]="$line"
400
401    elif [[ "$(echo $line | cut -c1-3)" = "IC:" ]]
402    then
403
404          # LINE DEFINES INPUT-COMMAND
405       (( iic = iic + 1 ))
406       line=$(echo $line | cut -c4-)
407       in_command[$iic]="$line"
408
409    elif [[ "$(echo $line | cut -c1-3)" = "OC:" ]]
410    then
411
412          # LINE DEFINES OUTPUT-COMMAND
413       (( ioc = ioc + 1 ))
414       line=$(echo $line | cut -c4-)
415       out_command[$ioc]="$line"
416
417    else
418
419          # SKIP ALL OTHER LINES
420       continue
421
422    fi
423
424 done < $config_file
425
426
427    # CHECK SETTING OF REQUIRED PARAMETERS
428 if [[ "$compiler_name" = "" ]]
429 then
430    printf "\n  +++ no compiler name found in $config_file"
431    printf "\n      Please add line \"compiler_name ...\" to that file."
432    locat=config_file; exit
433 fi
434 if [[ "$compiler_name_ser" = "" ]]
435 then
436    printf "\n  +++ no compiler name for non-paralle compilation found in $config_file"
437    printf "\n      Please add line \"compiler_name_ser ...\" to that file."
438    locat=config_file; exit
439 fi
440 if [[ "$compiler_options" = "" ]]
441 then
442    printf "\n  +++ no compiler options found in $config_file"
443    printf "\n      Please add line \"compiler_options ...\" to that file."
444    locat=config_file; exit
445 fi
446 if [[ "$linker_options" = "" ]]
447 then
448    printf "\n  +++ no linker options found in $config_file"
449    printf "\n      Please add line \"linker_options ...\" to that file."
450    locat=config_file; exit
451 fi
452 if [[ "$execute_command" = "" ]]
453 then
454    printf "\n  +++ no execute command found in $config_file"
455    printf "\n      Please add line \"execute_command ...\" to that file."
456    locat=config_file; exit
457 fi
458
459 if [[ "$hostfile" != "" ]]
460 then
461    if [[ $hostfile != auto  &&  ! -f $hostfile ]]
462    then
463       printf "\n  +++ no hostfile \"$hostfile\" found"
464       printf "\n      Please check line \"hostfile ...\" in $config_file"
465       locat=config_file; exit   
466    fi
467 fi
468
469
470    # DETERMINE THE CALL STATUS
471 if [[ "$return_address" != "" ]]
472 then
473 
474       # I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN
475       # BATCH MODE AND ...
476    running_on_remote=true
477 
478 else
479
480       # I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST
481     if [[ "$remote_ip" != "" ]]
482     then
483
484           # I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST
485        create_remote_batch_job=true
486
487     fi
488     running_on_remote=false
489 fi
490
491
492
493    # READ AND EVALUATE THE I/O-FILE LIST
494 [[ $silent = false ]]  &&  printf "\n    Reading the I/O files... "
495
496    # READ THE FILE CONNECTION FILE LINE BY LINE
497 while  read line
498 do
499
500       # FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
501    eval  line=\"$line\"
502
503
504       # INTERPRET THE LINE
505    if [[ "$(echo $line)" = "" ]]
506    then
507          # EMPTY LINE, NO ACTION
508       continue
509
510    elif [[ "$(echo $line | cut -c1)"  =  "#" ]]
511    then
512
513          # LINE IS A COMMENT LINE
514       true
515
516    else
517
518          # LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
519          # s2a: in/out - field
520          # s2b: loc    - field (optional)
521          # s2c: tr/ar  - field (optional)
522       s1=`echo $line | cut -d" " -f1`
523       s2=`echo $line | cut -d" " -s -f2`
524       s2a=$(echo $s2 | cut -d":" -f1)
525       if [[ $(echo $s2 | grep -c ":") = 0 ]]
526       then
527          s2b=""
528          s2c=""
529       else
530          s2b=`echo $s2 | cut -d":" -f2 | sed 's/:/ /g'`
531          s2c=`echo $s2 | cut -d":" -s -f3 | sed 's/:/ /g'`
532       fi
533       s3=`echo $line | cut -d" " -f3`
534       s4=`echo $line | cut -d" " -s -f4`
535       s5=`echo $line | cut -d" " -s -f5`
536       s6=`echo $line | cut -d" " -s -f6`
537
538       
539          # STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
540          # INPUT- OR OUTPUT-LIST.
541          # VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
542          # IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
543          # LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b = loc), THE FILE CONNECTION
544          # IS NOT CHECKED AND STORED.
545       IFSALT="$IFS"; IFS="$IFS:"
546       if [[ "$s2a" = in  &&  ! ( $create_remote_batch_job = true  &&  ( "$s2b" = loc  ||  "$s2b" = locopt ) ) ]]
547       then
548          found=false
549          for  actual  in  $activation_string_list
550          do
551             for  formal  in  $s3
552             do
553                [[ $actual = $formal  ||  "$formal" = "-" ]]  &&  found=true
554             done
555          done
556          if [[ $found = true ]]
557          then
558             (( iin = iin + 1 ))
559             localin[$iin]=$s1; transin[$iin]=$s2b; actionin[$iin]=$s2c;
560             typein[$iin]=$s3; pathin[$iin]=$s4; endin[$iin]=$s5;
561             extin[$iin]=$s6
562          fi
563       elif [[ "$s2a" = out  &&  ! ( $create_remote_batch_job = true  &&  "$s2b" = loc ) ]]
564       then
565          found=false
566          for  actual  in  $activation_string_list
567          do
568             for  formal  in  $s3 
569             do
570                [[ $actual = $formal  ||  "$formal" = "-"  ]]  &&  found=true
571             done
572          done
573          if [[ $found = true ]]
574          then
575             (( iout = iout + 1 ))
576             localout[$iout]=$s1; actionout[$iout]=$s2c; typeout[$iout]=$s3;
577             pathout[$iout]=$s4; endout[$iout]=$s5; extout[$iout]=$s6
578          fi
579       elif [[ "$s2a" != in  &&  "$s2a" != out ]]
580       then
581          printf "\n  +++ I/O-attribute in configuration file $config_file has the invalid"
582          printf "\n      value \"$s2\". Only \"in\" and \"out\" are allowed!"
583          locat=connect; exit
584       fi
585       IFS="$IFSALT"
586    fi
587
588 done < $fileconnection_file
589
590
591
592    # VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
593 [[ $palmrun_memory     != ""   ]]  &&  memory=$palmrun_memory
594 [[ $palmrun_cpumax     != ""   ]]  &&  cpumax=$palmrun_cpumax
595 [[ "$palmrun_cores" != ""  ]]  &&  cores=$palmrun_cores
596 [[ "$max_par_io_str" != "" ]]  &&  maximum_parallel_io_streams=$max_par_io_str
597 [[ "$palmrun_tasks_per_node" != "" ]]  &&  tasks_per_node=$palmrun_tasks_per_node
598
599
600
601      # EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
602 if [[ $run_coupled_model = true ]] 
603 then
604
605    cores_atmos=`echo $coupled_dist | cut -d" " -s -f1`
606    cores_ocean=`echo $coupled_dist | cut -d" " -s -f2`
607
608    if (( $cores_ocean + $cores_atmos != $cores ))
609    then
610
611       printf "\n  +++ number of processors does not fit to specification by \"-Y\"."
612       printf "\n      PEs (total)     : $cores"
613       printf "\n      PEs (atmosphere): $cores_atmos"
614       printf "\n      PEs (ocean)     : $cores_ocean"
615       locat=coupling; exit
616
617    fi
618
619 fi
620
621
622    # IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES
623    # HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_...
624    # FOLDER
625 if [[ $running_in_batch_mode = true ]]
626 then
627 
628    if [[ ! -d ${fast_io_catalog}/${sources_for_run_catalog} ]]
629    then
630       printf "\n  +++ directory ${fast_io_catalog}/${sources_for_run_catalog} is missing"
631       printf "\n      Please check the output of the palmrun-call"
632       printf "\n      that you did on your local host."
633       locat=SOURCES_FOR_RUN; exit
634    fi
635
636 else
637
638       # CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN
639       # AUTOMATIC RESTART RUN
640       # AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
641    if [[ $restart_run = false ]]
642    then
643
644          # COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON
645          # THE LOCAL HOST
646       if [[ ! -d $source_path ]]
647       then
648          printf "\n\n  +++ source path \"$source_path\" on local host"
649          printf "\n      \"$(hostname)\" does not exist"
650          locat=source_path; exit
651       fi
652
653       rm -rf   $sources_for_run_catalog
654       mkdir -p $sources_for_run_catalog
655
656       if [[ "$source_list" = LM ]]
657       then
658
659             # DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
660          source_list=""
661          cd  $source_path
662
663
664             # CHECK, IF TRUNK-DIRECTORY IS UNDER SVN CONTROL
665          if [[ ! -d ../.svn ]]
666          then
667             printf "\n\n  +++ source directory"
668             printf "\n         \"$source_path\" "
669             printf "\n         is not under control of \"subversion\"."
670             printf "\n         Please do not use palmrun-option \"-s LM\"\n"
671          fi
672
673
674             # LIST ALL MODIFIED SOURCE CODE FILES
675          Filenames=""
676          svn status  >  tmp_svnstatus
677          while  read line
678          do
679             firstc=`echo $line | cut -c1`
680             if [[ $firstc = M  ||  $firstc = "?" ]]
681             then
682                Name=`echo "$line" | cut -c8-`
683                extension=`echo $Name | cut -d. -f2`
684                if [[ "$extension" = f90 || "$extension" = F90 || "$extension" = f || "$extension" = F || "$extension" = c ]]
685                then
686                   Filenames="$Filenames "$Name
687                fi
688             fi
689          done < tmp_svnstatus
690          rm -rf  tmp_svnstatus
691
692
693             # COPY FILES TO SOURCES_FOR_RUN_...
694          for  filename  in  $Filenames
695          do
696             cp  $filename  ${working_directory}/${sources_for_run_catalog}
697             source_list=$source_list"$filename "
698          done
699
700          cd -  > /dev/null
701
702
703          # COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
704       elif [[ "$source_list" != "" ]]
705       then
706
707          cd  $source_path
708
709          for  filename  in  $source_list
710          do
711
712                # SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
713             if [[ $(echo $filename | grep -c "/") != 0 ]]
714             then
715                printf "\n  +++ source code file:  $filename"
716                printf "\n      must not contain (\"/\") "
717                locat=source; exit
718             fi
719
720             if [[ ! -f $filename ]]
721             then
722                printf "\n  +++ source code file:  $filename"
723                printf "\n      does not exist"
724                locat=source; exit
725             else
726                cp  $filename  ${working_directory}/${sources_for_run_catalog}
727             fi
728
729          done
730
731          cd -  > /dev/null
732
733       fi
734
735          # CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
736       [[ "$makefile" = "" ]]  &&  makefile=$source_path/Makefile
737       if [[ ! -f $makefile ]]
738       then
739          printf "\n  +++ file \"$makefile\" does not exist"
740          locat=make; exit
741       else
742          cp  $makefile  ${sources_for_run_catalog}/Makefile
743       fi
744
745
746          # COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
747       if [[ "$user_source_path" != "" ]]
748       then
749
750             # DOES THE DIRECTORY EXIST?
751          if [[ ! -d $user_source_path ]]
752          then
753
754             printf "\n\n  *** INFORMATIVE: additional source code directory"
755             printf "\n      \"$user_source_path\" "
756             printf "\n      does not exist or is not a directory."
757             printf "\n      No source code will be used from this directory!\n"
758             user_source_path=""
759             if [[ $silent == false ]]
760             then
761                sleep 2
762             fi
763
764          else
765
766             cd $user_source_path
767             found=false
768
769             Names=$(ls -1 *.f90 2>&1)
770             [[ $(echo $Names | grep -c '*.f90') = 0 ]]  &&  AddFilenames="$Names"
771             Names=$(ls -1 *.F90 2>&1)
772             [[ $(echo $Names | grep -c '*.F90') = 0 ]]  &&  AddFilenames="$AddFilenames $Names"
773             Names=$(ls -1 *.F 2>&1)
774             [[ $(echo $Names | grep -c '*.F') = 0   ]]  &&  AddFilenames="$AddFilenames $Names"
775             Names=$(ls -1 *.f 2>&1)
776             [[ $(echo $Names | grep -c '*.f') = 0   ]]  &&  AddFilenames="$AddFilenames $Names"
777             Names=$(ls -1 *.c 2>&1)
778             [[ $(echo $Names | grep -c '*.c') = 0   ]]  &&  AddFilenames="$AddFilenames $Names"
779
780             cd -  > /dev/null
781             cd  $sources_for_run_catalog
782
783                # COPY MAKEFILE IF EXISTING
784             if [[ -f $user_source_path/Makefile ]]
785             then
786                printf "\n\n  *** user Makefile from directory"
787                printf "\n      \"$user_source_path\" is used \n"
788                if [[ $silent == false ]]
789                then
790                   sleep 1
791                fi
792                cp  $user_source_path/Makefile  .
793             fi
794
795             for  filename  in  $AddFilenames
796             do
797                if [[ -f $filename ]]
798                then
799                   printf "\n  +++ source code file \"$filename\" found in additional"
800                   printf "\n      source code directory \"$user_source_path\" "
801                   printf "\n      but was also given with option \"-s\" which means that it should be taken"
802                   printf "\n      from directory \"$source_path\"."
803                   locat=source; exit
804                fi
805
806                cp  $user_source_path/$filename  .
807                source_list="$source_list $filename"
808
809                   # CHECK IF FILE IS CONTAINED IN MAKEFILE
810                if [[ $(grep -c $filename Makefile) = 0 ]]
811                then
812                   printf "\n\n  +++ user file \"$filename\" "
813                   printf "\n      is not listed in Makefile \n"
814                   locat=source; exit
815                else
816
817                   if [[ $found = false ]]
818                   then
819                      found=true
820                      printf "\n\n  *** following user file(s) added to the"
821                      printf " files to be translated:\n      "
822                   fi
823                   printf "$filename  "
824                   if [[ $silent == false ]]
825                   then
826                      sleep 0.5
827                   fi
828
829                fi
830             done
831             [[ $found = true ]]  &&  printf "\n"
832             cd -  > /dev/null
833          fi
834       fi
835
836          # COPY CONFIGURATION FILES
837       cp  $config_file  $sources_for_run_catalog
838       cp  $fileconnection_file  $sources_for_run_catalog
839
840          # COPY SHELLSCRIPTS
841       cp  ${source_path}/../SCRIPTS/palmrun    $sources_for_run_catalog
842       cp  ${source_path}/../SCRIPTS/batch_scp  $sources_for_run_catalog
843
844    fi
845
846 fi
847
848    # GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
849    # (HANDED OVER TO RESTART-RUNS USING OPTION -G)
850 if [[ "$global_revision" = "" ]]
851 then
852    global_revision=`svnversion $source_path  2>/dev/null`
853    global_revision="Rev: $global_revision"
854 fi
855
856
857    # IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
858 if [[ -n $cores ]]
859 then
860
861       # CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
862       # INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
863    if [[ $tasks_per_node = 0 ]]
864    then
865       printf "\n"
866       printf "\n  +++ option \"-T\" (tasks per node) is missing"
867       printf "\n      set -T option or define tasks_per_node in the config file"
868       locat=tasks_per_node; (( iec = 0 )); exit
869    fi
870
871    if (( cores < tasks_per_node ))
872    then
873       printf "\n"
874       printf "\n  +++ tasks per node (-T) cannot exceed total number of cores (-X)"
875       printf "\n      given values: -T $tasks_per_node  -X $cores"
876       locat=tasks_per_node; (( iec = 0 )); exit
877    fi
878
879    (( nodes = cores / ( tasks_per_node * threads_per_task ) ))
880    (( mpi_tasks = cores / threads_per_task ))
881    [[ $mpi_tasks = 0 ]]  &&  (( mpi_tasks = 1 ))
882    (( ii = cores / tasks_per_node ))
883    (( remaining_cores =  cores - ii * tasks_per_node ))
884    if (( remaining_cores > 0 ))
885    then
886       printf "\n"
887       printf "\n  +++ WARNING: tasks per node (option \"-T\") is not an integral"
888       printf "\n      divisor of the total number of cores (option \"-X\")"
889       printf "\n      values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\""
890       printf "\n      One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks"
891       (( nodes = nodes + 1 ))
892    fi
893
894       # SET THE TOTAL NUMBER OF NODES, REQUIRED FOR THE SUBJOB-COMMAND (SEE FURTHER BELOW)
895    if [[ "$tasks_per_node" != "" ]]
896    then
897       TOPT="-T $tasks_per_node"
898    fi
899
900 fi
901
902
903    # SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
904 if [[ "$maximum_parallel_io_streams" = "" ]]
905 then
906    maximum_parallel_io_streams=$cores
907 fi
908
909
910    # SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT
911 if [[ "$scp_port" != "" ]]
912 then
913    PORTOPT="-P $scp_port"
914    SSH_PORTOPT="-p $scp_port"
915 fi
916
917
918    # DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
919    # CONFIG-FILE
920 if [[ "$ssh_key" != "" ]]
921 then
922    ssh_key="-i $HOME/.ssh/$ssh_key"
923 fi
924
925
926    # SET QUEUE, IF NOT GIVEN
927 if [[ $create_batch_job = true  ||  $create_remote_batch_job = true ]]
928 then
929
930    if [[ $queue = none  &&  "$defaultqueue" = "" ]]
931    then
932       printf "\n"
933       printf "\n  +++ no default queue given in configuration file and no queue"
934       printf "\n      given with option -q"
935    fi
936    if [[ $queue = none ]]
937    then
938       queue=$defaultqueue
939    fi
940
941 fi
942
943
944    # GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
945    # CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
946 (( i = 0 ))
947 while (( i < iin ))
948 do
949    (( i = i + 1 ))
950    (( maxcycle = 0 ))
951
952       # GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
953       # FILE IDENTIFIER IS NOT PART OF THE FILENAME))
954    if [[ "${actionin[$i]}" = di ]]
955    then
956       remotepathin[$i]=${pathin[$i]}/${endin[$i]}  # EVALUATE REMOTE-PATH ON THE REMOTE
957                                                    # HOST ONLY
958       eval filename=${pathin[$i]}/${endin[$i]}
959    else
960       remotepathin[$i]=${pathin[$i]}/${fname}${endin[$i]}  # EVALUATE REMOTE-PATH ON THE REMOTE
961                                                             # HOST ONLY
962       eval filename=${pathin[$i]}/${fname}${endin[$i]}
963    fi
964    eval pathname=${pathin[$i]}
965
966       # CHECK IF FILE EXISTS
967    if ! ls $filename* 1>/dev/null 2>&1
968    then
969
970          # FILES WITH ATTRIBUTE locopt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
971       if [[ "${transin[$i]}" != "locopt" ]]
972       then
973          printf "\n\n  +++ INPUT-file: "
974          if [[ "${extin[$i]}" = ""  ||  "${extin[$i]}" = " " ]]
975          then
976             printf "\n           $filename"
977          else
978             printf "\n           $filename.${extin[$i]}"
979          fi
980          printf "\n      does not exist\n"
981          locat=input; exit
982       else
983          transin[$i]="unavailable"
984       fi
985    else
986
987          # DETERMINE THE FILE'S CYCLE NUMBER
988       ls -1 -d $filename    >   filelist  2>/dev/null
989       ls -1 -d $filename.*  >>  filelist  2>/dev/null
990       while  read line
991       do
992              # filename without path (i.e. after the last "/")
993           basefilename=$(basename ${line})
994
995              # check if there is an extension
996           extension=${basefilename##*.}
997           if [[ "$extension" = "${extin[$i]}" ]]
998           then
999              basefilename=${basefilename%.*}
1000           fi
1001
1002              # check for an existing cycle number
1003           cycle=${basefilename##*.}
1004           if [[ $cycle =~ ^-?[0-9]+$ ]]
1005           then
1006              (( icycle = $cycle ))
1007           else
1008              (( icycle = 0 ))
1009           fi
1010
1011           if (( icycle > maxcycle ))
1012           then
1013              (( maxcycle = icycle ))
1014           fi
1015
1016       done <filelist
1017       rm filelist
1018
1019          # APPEND CYCLE NUMBER TO FILENAME
1020       if (( maxcycle > 0 ))
1021       then
1022          if [[ "${extin[$i]}" != " "  &&   "${extin[$i]}" != "" ]]
1023          then
1024             filename=${filename}.$maxcycle.${extin[$i]}
1025          else
1026             filename=${filename}.$maxcycle
1027          fi
1028       else
1029          if [[ "${extin[$i]}" != " "  &&   "${extin[$i]}" != "" ]]
1030          then
1031             filename=${filename}.${extin[$i]}
1032          fi
1033       fi
1034       
1035          # STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1036          # IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
1037       absnamein[$i]=$filename
1038       if (( maxcycle > 0 ))
1039       then
1040          if [[ "${actionin[$i]}" = di ]]
1041          then
1042             frelin[$i]=${endin[$i]}.$maxcycle
1043          else
1044             frelin[$i]=${fname}${endin[$i]}.$maxcycle
1045          fi
1046       else
1047          if [[ "${actionin[$i]}" = di ]]
1048          then
1049             frelin[$i]=${endin[$i]}
1050          else
1051             frelin[$i]=${fname}${endin[$i]}
1052          fi
1053       fi
1054
1055    fi
1056 done
1057
1058   
1059    # GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
1060    # CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
1061    # OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED 
1062    # THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRASFERRED FROM THE REMOTE TO
1063    # THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
1064    # REMOTE HOST)
1065 (( i = 0 ))
1066 while (( i < iout ))
1067 do
1068    (( i = i + 1 ))
1069    if [[ ! ( $running_on_remote = true  &&  ( "${actionout[$i]}" = tr || "${actionout[$i]}" = tra || "${actionout[$i]}" = trpe ) ) ]]
1070    then
1071       if [[ "${actionout[$i]}" = tr ]]
1072       then
1073          actionout[$i]=""
1074       elif [[ "${actionout[$i]}" = trpe ]]
1075       then
1076          actionout[$i]=pe
1077       elif [[ "${actionout[$i]}" = tra ]]
1078       then
1079          actionout[$i]=a
1080       fi
1081       (( maxcycle = 0 ))
1082       eval filename=${pathout[$i]}/${fname}${endout[$i]}
1083       eval catalogname=${pathout[$i]}
1084       if ! ls $filename* 1>/dev/null 2>&1
1085       then
1086     
1087             # IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
1088          if  cat /dev/null > $filename 
1089          then
1090             rm  $filename
1091          else
1092
1093                # CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
1094                # IF IT DOES NOT EXIST, TRY TO CREATE IT
1095             if [[ ! -d $catalogname ]]
1096             then
1097                if  mkdir -p  $catalogname
1098                then
1099                   printf "\n\n  *** directory:"
1100                   printf "\n           $catalogname"
1101                   printf "\n      was created\n"
1102                else
1103                   printf "\n\n  +++ OUTPUT-file:"
1104                   printf "\n           $filename"
1105                   printf "\n      cannot be created, because directory does not exist"
1106                   printf "\n      and cannot be created either"
1107                   printf "\n"
1108                   locat=output  ; exit
1109                fi 2>/dev/null
1110             else
1111                printf "\n\n  +++ OUTPUT-file:"
1112                printf "\n           $filename"
1113                printf "\n      cannot be created, although directory exists"
1114                printf "\n"
1115                locat=output  ; exit
1116             fi
1117          fi 2>/dev/null
1118       else
1119
1120             # DETERMINE THE CYCLE NUMBER
1121          ls -1 -d $filename    >   filelist  2>/dev/null
1122          ls -1 -d $filename.*  >>  filelist  2>/dev/null
1123          while  read line
1124          do
1125
1126                # filename without path (i.e. after the last "/")
1127             basefilename=$(basename ${line})
1128
1129                # check if there is an extension
1130             extension=${basefilename##*.}
1131             if [[ "$extension" = "${extout[$i]}" ]]
1132             then
1133                basefilename=${basefilename%.*}
1134             fi
1135
1136                # check for an existing cycle number
1137             cycle=${basefilename##*.}
1138             if [[ $cycle =~ ^-?[0-9]+$ ]]
1139             then
1140                (( icycle = $cycle + 1 ))
1141             else
1142                (( icycle = 1 ))
1143             fi
1144
1145             if (( icycle > maxcycle ))
1146             then
1147                (( maxcycle = icycle ))
1148             fi
1149
1150          done <filelist
1151          rm filelist
1152       fi
1153
1154          # APPEND CYCLE NUMBER TO FILENAME AND CHECK, IF FILE CAN BE CREATED
1155          # IN CASE OF FILE-APPEND, FILE MUST BE APPENDED TO THE ONE WITH HIGHEST CYCLE NUMBER
1156       if [[ "${actionout[$i]}" != a ]]
1157       then
1158          if (( maxcycle > 0 ))
1159          then
1160             filename_tmp=${filename}.$maxcycle
1161             if  cat /dev/null > $filename_tmp 
1162             then
1163                rm  $filename_tmp
1164             else
1165                printf "\n  +++ OUTPUT-file:"
1166                printf "\n           $filename_tmp"
1167                printf "\n      cannot be created"
1168                locat=output  ; exit
1169             fi
1170          fi
1171       else
1172          (( maxcycle = maxcycle - 1 ))
1173       fi
1174       
1175       (( cycnum[$i] = maxcycle ))
1176       pathout[$i]=$filename
1177
1178    fi
1179 done
1180
1181
1182    # DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY
1183 if [[ $running_in_batch_mode = false ]]
1184 then
1185    run_id=$RANDOM
1186    job_id=${fname}.$run_id
1187
1188    TEMPDIR=$fast_io_catalog/$job_id
1189 fi
1190
1191
1192    # CHECK SETTINGS REQUIRED FOR BATCH JOBS
1193 if [[ $create_batch_job = true  ||  $create_remote_batch_job = true ]]
1194 then
1195
1196       # CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE
1197    if [[ $ibd = 0 ]]
1198    then
1199       printf "\n"
1200       printf "\n  +++ no batch directives found in configuration file"
1201       locat=config_file_batch_directives; (( iec = 0 )); exit
1202    fi
1203
1204       # CHECK IF CPUTIME IS GIVEN FOR JOB
1205    done=false
1206    cputime=$cpumax
1207    while [[ $done = false ]]
1208    do
1209       if (( cputime == 0 ))
1210       then
1211          printf "\n  +++ cpu-time is undefined"
1212          printf "\n  >>> Please type CPU-time in seconds as INTEGER:"
1213          printf "\n  >>> "
1214          read  cputime   1>/dev/null  2>&1
1215       else
1216          done=true
1217       fi
1218    done
1219    cpumax=$cputime
1220
1221       # CHECK THE MEMORY DEMAND
1222    done=false
1223    while [[ $done = false ]]
1224    do
1225       if (( memory == 0 ))
1226       then
1227          printf "\n  +++ memory demand is undefined"
1228          printf "\n  >>> Please type memory in  MByte per process  as INTEGER:"
1229          printf "\n  >>> "
1230          read  memory  1>/dev/null  2>&1
1231       else
1232          done=true
1233       fi
1234    done
1235
1236       # IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
1237    if [[ $create_remote_batch_job = true  &&  -z $remote_username ]]
1238    then
1239       while [[ -z $remote_username ]]
1240       do
1241          printf "\n  +++ username on remote host with IP \"$remote_ip\" is undefined"
1242          printf "\n  >>> Please type username:"
1243          printf "\n  >>> "
1244          read  remote_username
1245       done
1246    fi
1247
1248 else
1249
1250    if [[ $running_in_batch_mode = false ]]
1251    then
1252       cputime=10000000  # NO LIMT FOR INTERACTIVE RUNS
1253       cpumax=$cputime
1254    else
1255       cputime=$cpumax
1256    fi
1257
1258 fi
1259
1260
1261    # CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES
1262 (( cpu_hours  = cputime / 3600 ))
1263 (( resttime = cputime - cpu_hours * 3600 ))
1264 (( cpu_minutes  = resttime / 60 ))
1265 (( cpu_seconds = resttime - cpu_minutes * 60 ))
1266 timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds}
1267
1268
1269    # OUTPUT OF THE PALMRUN-HEADER
1270 calltime=$(date)
1271 printf "\n"
1272 printf "#------------------------------------------------------------------------# \n"
1273 printf "| %-35s%35s | \n" "$version" "$calltime"
1274 printf "|                                                                        | \n"
1275 column1="called on:"; column2=$(hostname)
1276 printf "| %-25s%-45s | \n" "$column1" "$column2"
1277 if [[ $create_remote_batch_job = true ]]
1278 then
1279    column1="execution on:"; column2="$host_configuration (username: $remote_username)"
1280 else
1281    if [[ $running_on_remote = true ]]
1282    then
1283       column1="execution on:"; column2="$host_configuration (IP:$remote_ip)"
1284    else
1285       column1="execution on:"; column2="$host_configuration (IP:$local_ip)"
1286    fi
1287 fi
1288 printf "| %-25s%-45s | \n" "$column1" "$column2"
1289
1290 column1="running in:"
1291 if [[ $running_in_batch_mode = true ]]
1292 then
1293    column2="batch job mode"
1294 else
1295    if [[ $create_batch_job = true  ||  $create_remote_batch_job = true ]]
1296    then
1297       column2="job creation mode"
1298    else
1299       column2="interactive run mode"
1300    fi
1301 fi
1302 printf "| %-25s%-45s | \n" "$column1" "$column2"
1303
1304 if  [[ $running_in_batch_mode = true  ||  $create_batch_job = true  ||  $create_remote_batch_job = true ]]
1305 then
1306    if [[ "$project_account" != "" ]]
1307    then
1308       column1="project account number:"
1309       column2="$project_account"
1310       printf "| %-25s%-45s | \n" "$column1" "$column2"
1311    fi
1312 fi
1313
1314 if [[ -n $cores ]]
1315 then
1316    if [[ $run_coupled_model = false ]]
1317    then
1318       column1="number of cores:"; column2=$cores
1319    else
1320       column1="number of cores:"; column2="$cores  (atmosphere: $cores_atmos, ocean: $cores_ocean)"
1321    fi
1322    printf "| %-25s%-45s | \n" "$column1" "$column2"
1323 fi
1324 if [[ -n $tasks_per_node ]]
1325 then
1326    column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)"
1327    printf "| %-25s%-45s | \n" "$column1" "$column2"
1328    if (( remaining_cores > 0 ))
1329    then
1330       column1=" "; column2="one of the nodes only filled with $remaining_cores tasks"
1331       printf "| %-25s%-45s | \n" "$column1" "$column2"
1332    fi
1333 fi
1334 if [[ $maximum_parallel_io_streams != $cores ]]
1335 then
1336    column1="max par io streams:"; column2="$maximum_parallel_io_streams"
1337    printf "| %-25s%-45s | \n" "$column1" "$column2"
1338 fi
1339 if [[ $use_openmp = true ]]
1340 then
1341    column1="threads per task:"; column2="$threads_per_task"
1342    printf "| %-25s%-45s | \n" "$column1" "$column2"
1343 fi
1344 if [[ $create_batch_job = true  ||  $create_remote_batch_job = true  ||  $running_in_batch_mode = true ]]
1345 then
1346    column1="memory demand / PE":; column2="$memory MB"
1347    printf "| %-25s%-45s | \n" "$column1" "$column2"
1348    column1="job cpu time (h:m:s):"; column2="$timestring"
1349    printf "| %-25s%-45s | \n" "$column1" "$column2"
1350 fi
1351 printf "|                                                                        | \n"
1352 if [[ "$source_list" != "" ]]
1353 then
1354    if [[ "$make_options" != "" ]]
1355    then
1356       column1="make options:"; column2=$(echo "$make_options" | cut -c-45)
1357       printf "| %-25s%-45s | \n" "$column1" "$column2"
1358       line=$(echo "$make_options" | cut -c46-)
1359       while [[ "$line" != "" ]]
1360       do
1361          column1=""
1362          column2=$(echo "$line" | cut -c-45)
1363          printf "| %-25s%-45s | \n" "$column1" "$column2"
1364          line=$(echo "$line" | cut -c46-)
1365       done
1366    fi
1367 fi
1368
1369 column1="cpp directives:"; column2=$(echo "$cpp_options" | cut -c-45)
1370 printf "| %-25s%-45s | \n" "$column1" "$column2"
1371 line=$(echo "$cpp_options" | cut -c46-)
1372 while [[ "$line" != "" ]]
1373 do
1374    column1=""
1375    column2=$(echo "$line" | cut -c-45)
1376    printf "| %-25s%-45s | \n" "$column1" "$column2"
1377    line=$(echo "$line" | cut -c46-)
1378 done
1379
1380 column1="compiler options:"; column2=$(echo "$compiler_options" | cut -c-45)
1381 printf "| %-25s%-45s | \n" "$column1" "$column2"
1382 line=$(echo "$compiler_options" | cut -c46-)
1383 while [[ "$line" != "" ]]
1384 do
1385    column1=""
1386    column2=$(echo "$line" | cut -c-45)
1387    printf "| %-25s%-45s | \n" "$column1" "$column2"
1388    line=$(echo "$line" | cut -c46-)
1389 done
1390
1391 column1="linker options:"; column2=$(echo "$linker_options" | cut -c-45)
1392 printf "| %-25s%-45s | \n" "$column1" "$column2"
1393 line=$(echo "$linker_options" | cut -c46-)
1394 while [[ "$line" != "" ]]
1395 do
1396    column1=""
1397    column2=$(echo "$line" | cut -c-45)
1398    printf "| %-25s%-45s | \n" "$column1" "$column2"
1399    line=$(echo "$line" | cut -c46-)
1400 done
1401
1402 if [[ "$login_init_cmd" != "" ]]
1403 then
1404    column1="login init commands:"; column2=$(echo "$login_init_cmd" | cut -c-45)
1405    printf "| %-25s%-45s | \n" "$column1" "$column2"
1406    line=$(echo "$login_init_cmd" | cut -c46-)
1407    while [[ "$line" != "" ]]
1408    do
1409       column1=""
1410       column2=$(echo "$line" | cut -c-45)
1411       printf "| %-25s%-45s | \n" "$column1" "$column2"
1412       line=$(echo "$line" | cut -c46-)
1413    done
1414 fi
1415
1416 if [[ "$module_commands" != "" ]]
1417 then
1418    column1="module commands:"; column2=$(echo "$module_commands" | cut -c-45)
1419    printf "| %-25s%-45s | \n" "$column1" "$column2"
1420    line=$(echo "$module_commands" | cut -c46-)
1421    while [[ "$line" != "" ]]
1422    do
1423       column1=""
1424       column2=$(echo "$line" | cut -c-45)
1425       printf "| %-25s%-45s | \n" "$column1" "$column2"
1426       line=$(echo "$line" | cut -c46-)
1427    done
1428 fi
1429 printf "|                                                                        | \n"
1430 column1="base name of files:"; column2=$fname
1431 printf "| %-25s%-45s | \n" "$column1" "$column2"
1432 column1="activation string list:"; column2=$(echo $activation_string_list)
1433 printf "| %-25s%-45s | \n" "$column1" "$column2"
1434
1435 if [[ "$ocean_file_appendix" = true ]]
1436 then
1437    printf "| %-35s%-35s | \n" "suffix \"_O\" is added to local files" " "
1438 fi
1439
1440 if [[ "$source_list" != "" ]]
1441 then
1442    printf "|                                                                        | \n"
1443    printf "| Files to be compiled:                                                  | \n"
1444    line=$source_list
1445    while [[ "$line" != "" ]]
1446    do
1447       linestart=$(echo $line | cut -c-70)
1448       printf "| %-70s | \n" "$linestart"
1449       line=$(echo "$line" | cut -c71-)
1450    done
1451 fi
1452 printf "#------------------------------------------------------------------------#"
1453
1454
1455
1456    # OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
1457 if [[ $do_trace = true ]]
1458 then
1459    (( i = 0 ))
1460    while (( i < iin ))
1461    do
1462       (( i = i + 1 ))
1463       if (( i == 1 ))
1464       then
1465          printf "\n\n >>> INPUT-file assignments:\n"
1466       fi
1467       printf "\n     ${localin[$i]} :  ${absnamein[$i]}"
1468    done
1469    (( i = 0 ))
1470    while (( i < iout ))
1471    do
1472       (( i = i + 1 ))
1473       if (( i == 1 ))
1474       then
1475          printf "\n\n >>> OUTPUT-file assignments:\n"
1476       fi
1477       printf "\n     ${localout[$i]} :  ${pathout[$i]}"
1478    done
1479    (( i = 0 ))
1480    while (( i < iic ))
1481    do
1482       (( i = i + 1 ))
1483       if (( i == 1 ))
1484       then
1485          printf "\n\n >>> INPUT-commands:\n"
1486       fi
1487       printf "\n     ${in_command[$i]}" 
1488    done
1489    (( i = 0 ))
1490    while (( i < ioc ))
1491    do
1492       (( i = i + 1 ))
1493       if (( i == 1 ))
1494       then
1495          printf "\n\n >>> OUTPUT-commands:\n"
1496       fi
1497       printf "\n     ${out_command[$i]}" 
1498    done
1499 fi
1500
1501    # QUERY FOR CONTINUE
1502 if [[ $silent = false  &&  $running_in_batch_mode = false ]]
1503 then
1504    antwort=dummy
1505    printf "\n\n"
1506    printf " >>> everything o.k. (y/n) ?  "
1507    while  read antwort
1508    do
1509       if [[ "$antwort" != y  &&  "$antwort" != Y  &&  "$antwort" != n  &&  "$antwort" != N ]]
1510       then
1511          printf " >>> everything o.k. (y/n) ?  "
1512       else
1513          break
1514       fi
1515    done
1516    if [[ $antwort = n  ||  $antwort = N ]]
1517    then
1518       locat=user_abort; (( iec = 0 )); exit
1519    fi
1520    if [[ $create_batch_job = true  ||  $create_remote_batch_job = true ]]
1521    then
1522       printf " ***  batch-job will be created and submitted"
1523    else
1524       printf " ***  PALMRUN will now continue to execute on this machine"
1525    fi
1526 fi
1527
1528 
1529
1530    # PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE
1531 if [[ $restart_run = false  &&  $running_in_batch_mode = false ]]
1532 then
1533
1534    if [[ $create_batch_job = true  ||  $create_remote_batch_job  = true ]]
1535    then
1536       printf "\n\n  *** creating executable and other sources for the remote host"
1537    else
1538       printf "\n\n  *** creating executable and other sources for the local host"
1539    fi
1540
1541       # FIRST CHECK, IF A MAKE DEPOSITORY EXISTS, AND IF NOT, ASK THE USER IF
1542       # IT SHALL BE CREATED
1543    ask_for_make_depository=false
1544    if [[ $create_remote_batch_job = true ]]
1545    then
1546
1547       line=`grep %base_directory $config_file`
1548       make_depository=`echo $line | cut -d" " -s -f2`/MAKE_DEPOSITORY_${host_configuration}
1549       echo  "[[ ! -d ${make_depository} ]]  &&  echo depository not found" | ssh  -q  $ssh_key  ${remote_username}@${remote_ip} 2>&1  | tee ${host_configuration}_last_make_protokoll
1550
1551       if [[ $(grep -c "depository not found" ${host_configuration}_last_make_protokoll) != 0 ]]
1552       then
1553          printf "\n\n  +++ make depository \"${make_depository}\""
1554          printf "\n      on remote host not found!"
1555          ask_for_make_depository=true
1556       fi
1557       rm ${host_configuration}_last_make_protokoll
1558
1559    else
1560
1561          # CHECK FOR MAKE_DEPOSITORY ON THE LOCAL HOST
1562       make_depository=${base_directory}/MAKE_DEPOSITORY_${host_configuration}
1563       if [[ ! -d ${make_depository} ]]
1564       then
1565          printf "\n\n  +++ make depository \"${make_depository}\""
1566          printf "\n      on local host not found!"
1567          ask_for_make_depository=true
1568       fi
1569
1570    fi
1571
1572    if [[ $ask_for_make_depository = true ]]
1573    then
1574
1575       antwort=dummy
1576       printf "\n\n"
1577       printf "  >>> Create a new one (y/n) ?  "
1578       while  read antwort
1579       do
1580          if [[ "$antwort" != y  &&  "$antwort" != Y  &&  "$antwort" != n  &&  "$antwort" != N ]]
1581          then
1582             printf "  >>> Create a new one (y/n) ?  "
1583          else
1584             break
1585          fi
1586       done
1587       if [[ $antwort = n  ||  $antwort = N ]]
1588       then
1589          locat=user_abort; (( iec = 0 )); exit
1590       fi
1591
1592       palmbuild  -v  -h $host_configuration
1593
1594       if [[ $? != 0 ]]
1595       then
1596   
1597              # ABORT IN CASE OF COMPILATION PROBLEMS
1598          printf "\n  +++ error while compiling for the MAKE_DEPOSITORY"
1599          locat=make_depository
1600          exit
1601       else
1602          echo "  *** now continue with creating executable and other sources"
1603       fi
1604
1605    fi
1606
1607    palmbuild  -v  $use_existing_sources_folder  -h $host_configuration  -d $fname
1608
1609    if [[ $? != 0 ]]
1610    then
1611
1612           # ABORT IN CASE OF COMPILATION PROBLEMS
1613       printf "\n  +++ error while creating executable and/or other sources"
1614       locat=execution
1615       rm -rf  $sources_for_run_catalog
1616       exit
1617
1618    else
1619
1620       printf "\n$dashes\n  *** executable and other sources created\n"
1621       rm -rf  $sources_for_run_catalog
1622
1623    fi
1624
1625 fi
1626
1627
1628    # NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
1629    # (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
1630 if [[ $create_batch_job = false  &&  $create_remote_batch_job = false ]]
1631 then
1632
1633       # CHANGE TO THE TEMPORARY WORKING DIRECTORY
1634    if [[ $running_in_batch_mode = false ]]
1635    then
1636          # CREATE THE DIRECTORY AND COPY FILES FROM SOURCES_FOR_RUN_... TO THAT
1637          # FOLDER
1638       mkdir -p  $TEMPDIR
1639       chmod  go+rx  $TEMPDIR
1640       tmpcreate=true
1641       cd  $TEMPDIR
1642       cp  ${fast_io_catalog}/${sources_for_run_catalog}/{*,.[!.]*}  $TEMPDIR
1643       printf "\n  *** changed to temporary directory: $TEMPDIR"
1644
1645    else
1646
1647          # IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR
1648       printf "\n  *** running in temporary directory: $TEMPDIR"
1649
1650    fi
1651
1652
1653       # PROVIDE THE INPUT FILES
1654       # LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
1655    (( i = 0 ))
1656    while (( i < iin ))
1657    do
1658       (( i = i + 1 ))
1659       if (( i == 1 ))
1660       then
1661          printf "\n\n  *** providing INPUT-files:\n$dashes"
1662       fi
1663
1664
1665          # SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
1666       if [[ "${transin[$i]}" = unavailable ]]
1667       then
1668          if [[ "${extin[$i]}" = ""  ||  "${extin[$i]}" = " " ]]
1669          then
1670             printf "\n  *** INFORMATIVE: input file \"${pathin[$i]}/${fname}${endin[$i]}\" "
1671             printf "\n                   is not available!"
1672          else
1673             printf "\n  *** INFORMATIVE: input file \"${pathin[$i]}/${fname}${endin[$i]}.${extin[$i]}\" "
1674             printf "\n                   is not available!"
1675          fi
1676          continue
1677       fi
1678
1679          # CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
1680       files_for_cores=false; filetype=file
1681       if [[ "${actionin[$i]}" = pe  &&  -n $cores ]]
1682       then
1683          files_for_cores=true; filetype=files
1684          actionin[$i]=""
1685       elif [[ "${actionin[$i]}" = pe  &&  ! -n $cores ]]
1686       then
1687          actionin[$i]=""
1688       elif [[ "${actionin[$i]}" = lnpe  &&  -n $cores ]]
1689       then
1690          files_for_cores=true; filetype=files
1691          actionin[$i]="ln"
1692       elif [[ "${actionin[$i]}" = lnpe  &&  ! -n $cores ]]
1693       then
1694          actionin[$i]="ln"
1695       fi
1696
1697       if [[ $files_for_cores = true ]]
1698       then
1699          printf "\n  >>> INPUT: ${absnamein[$i]}/....  to  ${localin[$i]}"
1700       else
1701          printf "\n  >>> INPUT: ${absnamein[$i]}  to  ${localin[$i]}"
1702       fi
1703
1704          # INPUT-FILES TO BE LINKED
1705       if [[ "${actionin[$i]}" = ln ]]
1706       then
1707
1708          printf "\n      $filetype will be linked"
1709          if [[ $files_for_cores = false ]]
1710          then
1711             if [[ -f "${absnamein[$i]}" ]]
1712             then
1713                ln  ${absnamein[$i]}  ${localin[$i]}
1714                got_tmp[$i]=true
1715             fi
1716          else
1717             if [[ -d "${absnamein[$i]}" ]]
1718             then
1719                mkdir -p ${localin[$i]}
1720                cd ${absnamein[$i]}
1721                for file in $(ls *)
1722                do
1723                   ln $file $TEMPDIR/${localin[$i]}
1724                done >|/dev/null 2>&1
1725                cd $TEMPDIR
1726             fi
1727
1728                # IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
1729             if [[ ! -f "${localin[$i]}/_000000" ]]
1730             then
1731                printf "\n  --- WARNING: ln failed, using cp instead (might be time consuming...)"
1732                cp -r  ${absnamein[$i]}/*  ${localin[$i]}
1733             fi
1734
1735             got_tmp[$i]=true
1736          fi
1737       fi
1738
1739          # FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
1740       if [[ "${actionin[$i]}" = ""  ||  "${actionin[$i]}" = "di"  ||  "${actionin[$i]}" = "npe" ]]
1741       then
1742
1743          if [[ "${actionin[$i]}" = "npe"  &&  -n $cores ]]
1744          then
1745
1746                # FILE COPIES ARE PROVIDED FOR ALL CORES
1747                # EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
1748             printf "\n      file will be provided for $cores processors"
1749             mkdir -p ${localin[$i]}
1750             ival=$cores
1751             (( ii = 0 ))
1752             while (( ii <= ival-1 ))
1753             do
1754                if (( ii < 10 ))
1755                then
1756                   cp  ${absnamein[$i]}  ${localin[$i]}/_000$ii
1757                elif (( ii < 100 ))
1758                then
1759                   cp  ${absnamein[$i]}  ${localin[$i]}/_00$ii
1760                elif (( ii < 1000 ))
1761                then
1762                   cp  ${absnamein[$i]}  ${localin[$i]}/_0$ii
1763                else
1764                   cp  ${absnamein[$i]}  ${localin[$i]}/_$ii
1765                fi
1766                (( ii = ii + 1 ))
1767             done
1768
1769          else
1770
1771             if [[ $files_for_cores = true ]]
1772             then
1773
1774                   # PROVIDE FILES FOR EACH CORE
1775                   # FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
1776                   # FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
1777                printf "\n      providing $cores files for the respective cores"
1778                mkdir -p ${localin[$i]}
1779                        if [[ $link_local_input = true ]]
1780                              then
1781                                 printf "      files will be linked\n"
1782                                 cd ${absnamein[$i]}
1783                                 for file in $(ls *)
1784                                 do
1785                                    ln -f $file  ${localin[$i]}
1786                                 done
1787                                 cd $TEMPDIR
1788                              fi
1789
1790                   # IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
1791                              if [[ ! -f "${localin[$i]}/_000000" ]]
1792                              then
1793                                 if [[ $link_local_input = true ]]
1794                                        then
1795                                        printf "\n  --- WARNING: ln failed, using cp instead (might be time consuming...)"
1796                                 fi
1797                                 cp -r  ${absnamein[$i]}/*  ${localin[$i]}
1798                              fi
1799
1800             else
1801
1802                   # PROVIDE FILE FOR RUNS ON A SINGLE CORE
1803                        if [[ $link_local_input = true ]]
1804                        then
1805                                 printf "      file will be linked\n"
1806                                 ln -f  ${absnamein[$i]}  ${localin[$i]}
1807                        fi
1808                                # If "ln -f" fails of if "$link_local_input = false" do a normal "cp"
1809                        if [[ ! -f "${localin[$i]}" ]]
1810                then
1811                                 if [[ $link_local_input = true ]]
1812                          then
1813                      printf "\n  --- WARNING: ln failed, using cp instead (might be time consuming...)"
1814                                 fi
1815                                 cp  ${absnamein[$i]}  ${localin[$i]}
1816                fi
1817             fi
1818          fi
1819       fi
1820
1821    done
1822    if (( i != 0 ))
1823    then
1824       printf "\n$dashes\n  *** all INPUT-files provided \n"
1825    fi
1826
1827
1828       # EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
1829    (( i = 0 ))
1830    while (( i < iic ))
1831    do
1832       (( i = i + 1 ))
1833       if (( i == 1 ))
1834       then
1835          printf "\n\n  *** execution of INPUT-commands:\n$dashes"
1836       fi
1837       printf "\n  >>> ${in_command[$i]}"
1838       eval  ${in_command[$i]}
1839       if (( i == iic ))
1840       then
1841          printf "\n$dashes\n"
1842       fi
1843    done
1844
1845
1846       # CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
1847       # (FILE ENVPAR WILL BE READ BY PALM)
1848    cat  >  ENVPAR  <<  EOF
1849 &envpar  run_identifier = '$fname', host = '$host_configuration',
1850          write_binary = .${write_binary}., tasks_per_node = $tasks_per_node,
1851          maximum_parallel_io_streams = $maximum_parallel_io_streams,
1852          maximum_cpu_time_allowed = ${cpumax}.,
1853          revision = '$global_revision',
1854          batch_job = .${running_in_batch_mode}. /
1855
1856EOF
1857
1858
1859       # STARTING THE EXECUTABLE
1860    printf "\n\n  *** execution starts in directory\n      \"`pwd`\"\n$dashes\n"
1861    PATH=$PATH:$TEMPDIR
1862
1863
1864       # REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES
1865    line=`echo  "${execute_command}" | sed 's/{{MPI_TASKS}}/$mpi_tasks/g' | sed 's/{{TASKS_PER_NODE}}/$tasks_per_node/g'`
1866    line2=`echo  "${execute_command}" | sed 's/{{MPI_TASKS}}/1/g' | sed 's/{{TASKS_PER_NODE}}/1/g' | sed 's/palm/combine_plot_fields.x/g'`
1867    eval line=\"$line\"
1868    execute_command="$line"
1869
1870
1871       # EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS
1872    eval line2=\"$line2\"
1873    execute_command_for_combine="$line2"
1874
1875
1876       # PROVIDE A HOSTFILE, IF REQUIRED
1877    if [[ "$hostfile" != "" ]]
1878    then
1879
1880       if [[ $hostfile = auto ]]
1881       then
1882             # CREATE A NEW HOSTFILE
1883          (( ii = 1 ))
1884          while (( ii <= cores / threads_per_task ))
1885          do
1886             echo  $(hostname)  >>  hostfile
1887             (( ii = ii + 1 ))
1888          done
1889          if (( cores / threads_per_task == 0 ))
1890          then
1891             echo  $(hostname)  >>  hostfile
1892          fi
1893       
1894       else
1895          cp  $hostfile  hostfile
1896       fi
1897       eval line=\"`head -n $ii  hostfile`\"
1898       printf "\n  *** running on: $line"
1899    fi
1900
1901
1902
1903       # SET THE NUMBER OF OPENMP-THREADS
1904    if [[ $use_openmp = true ]]
1905    then
1906       export OMP_NUM_THREADS=$threads_per_task
1907       printf "\n  *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS"
1908    else
1909       export OMP_NUM_THREADS=1
1910    fi
1911
1912
1913       # PROVIDE DATA FOR
1914    if [[ $run_coupled_model = false ]]
1915    then
1916       if [[ "$ocean_file_appendix" = true ]]
1917       then
1918          echo "precursor_ocean"  >  coupling_steering
1919       else
1920          echo "precursor_atmos"  >  coupling_steering
1921      fi
1922    else
1923       (( iia = $cores_atmos / $threads_per_task ))
1924       (( iio = $cores_ocean / $threads_per_task ))
1925       printf "\n      coupled run ($iia atmosphere, $iio ocean)"
1926       printf "\n\n"
1927       echo "coupled_run $iia $iio"  >  coupling_steering
1928    fi
1929
1930    printf "\n  *** execute command:"
1931    printf "\n      \"$execute_command\" \n\n"
1932
1933    $execute_command  <  coupling_steering
1934
1935    if [[ $? != 0 ]]
1936    then
1937
1938           # ABORT IN CASE OF RUNTIME ERRORS
1939       printf "\n  +++ runtime error occured"
1940       locat=execution
1941       exit
1942
1943    else
1944
1945       printf "\n$dashes\n  *** execution finished \n"
1946
1947    fi
1948
1949
1950       # CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
1951       # BY EACH CORE INTO ONE FILE
1952   if [[ ! -f combine_plot_fields.x ]]
1953   then
1954
1955      printf "\n\n\n  +++ WARNING: no combine_plot_fields found"
1956      printf "\n      2d- and/or 3d-data may be incomplete!"
1957      printf "\n      Your previous palmbuild may have failed. Please check.\n"
1958
1959   elif [[ "$combine_plot_fields" == true ]]
1960   then
1961
1962      printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..."
1963      $execute_command_for_combine
1964
1965   else
1966
1967         # TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
1968         # DATA OUTPUT. TO DO: EXTEND THIS BRANCH BY CREATING A BATCH JOB for combine_plot_fields.
1969         # ??? koennen wir das streichen ???
1970      printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
1971   fi
1972
1973
1974
1975       # EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
1976    (( i = 0 ))
1977    while (( i < ioc ))
1978    do
1979       (( i = i + 1 ))
1980       if (( i == 1 ))
1981       then
1982          printf "\n\n  *** execution of OUTPUT-commands:\n$dashes"
1983       fi
1984       printf "\n  >>> ${out_command[$i]}"
1985       eval  ${out_command[$i]}
1986       if (( i == ioc ))
1987       then
1988          printf "\n$dashes\n"
1989       fi
1990    done
1991
1992
1993       # IN TRACE-MODE PRINT CONTENTS OF THE CURRENT (TEMPORARY) WORKING DIRECTORY
1994    if [[ $do_trace = true ]]
1995    then
1996       printf "\n\n"
1997       ls -al
1998    fi
1999   
2000
2001       # COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
2002    (( i = 0 ))
2003    while (( i < iout ))
2004    do
2005       (( i = i + 1 ))
2006       if (( i == 1 ))
2007       then
2008          printf "\n\n  *** saving OUTPUT-files:"
2009
2010             # GET RUN NUMBER ASSIGNED BY PALM
2011          if [[ -f RUN_NUMBER ]]
2012          then
2013              read  run_number  <  RUN_NUMBER
2014              printf "\n  *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
2015              usecycle_option="-U $run_number"
2016          else
2017              run_number=0
2018              usecycle_option=""
2019          fi
2020          if [[ $running_on_remote = true  &&  "$remote_loginnode" != "" ]]
2021          then
2022             printf "\n  *** in case of SCP transfers to local host"
2023             printf "\n      they will be done via remote login-node \"$remote_loginnode\" "
2024          fi
2025          printf "\n$dashes"
2026       fi
2027
2028          # ADD CYCLE NUMBER TO FILENAME
2029       if [[ ! ( $running_on_remote = true  &&  ( "${actionout[$i]}" = tr || "${actionout[$i]}" = tra || "${actionout[$i]}" = trpe ) ) ]]
2030       then
2031
2032              # IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
2033          if [[ "${actionout[$i]}" != "a" ]]
2034          then
2035                # SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
2036                # WITH AN EXISTING CYCLE NUMBER
2037             if (( run_number >= cycnum[$i] ))
2038             then
2039                (( cycnum[$i] = run_number ))
2040             else
2041                if (( run_number > 0 ))
2042                then
2043                   printf "\n  --- INFORMATIVE: The following file cannot get a unified cycle number"
2044                fi
2045             fi
2046          fi
2047          if (( cycnum[$i] > 0 ))
2048          then
2049             pathout[$i]=${pathout[$i]}.${cycnum[$i]}
2050          fi
2051       fi           
2052
2053          # CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
2054       files_for_cores=false; filetype=file
2055       link_local_output=false
2056       if [[ "${actionout[$i]}" = pe  &&  -n $cores ]]
2057       then
2058          files_for_cores=true; filetype=directory
2059          actionout[$i]=""
2060       elif [[ "${actionout[$i]}" = pe  &&  ! -n $cores ]]
2061       then
2062          actionout[$i]=""
2063       elif [[ "${actionout[$i]}" = lnpe  &&  -n $cores ]]
2064       then
2065          files_for_cores=true; filetype=directory
2066          link_local_output=true
2067          actionout[$i]=""
2068       elif [[ "${actionout[$i]}" = lnpe  &&  ! -n $cores ]]
2069       then
2070          link_local_output
2071          actionout[$i]=""
2072       elif [[ "${actionout[$i]}" = trpe  &&  -n $cores ]]
2073       then
2074          files_for_cores=true; filetype=directory
2075          actionout[$i]="tr"
2076       elif [[ "${actionout[$i]}" = trpe  &&  ! -n $cores ]]
2077       then
2078          actionout[$i]="tr"
2079       fi
2080
2081       if [[ ! -f ${localout[$i]}  &&  $files_for_cores = false ]]
2082       then
2083          printf "\n  +++ temporary OUTPUT-file  ${localout[$i]}  does not exist\n"
2084       elif [[ ! -d ${localout[$i]}  &&  $files_for_cores = true ]]
2085       then
2086          printf "\n  +++ temporary OUTPUT-file  ${localout[$i]}/....  does not exist\n"
2087       else
2088
2089
2090             # COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
2091             # IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
2092          if [[ "${actionout[$i]}" = tr  ||  "${actionout[$i]}" = tra ]]
2093          then
2094             if [[ $running_on_remote = true ]]
2095             then
2096
2097                   # SET OPTIONS FOR TRANSFER
2098                if [[ "${actionout[$i]}" = tr ]]
2099                then
2100                   if [[ $files_for_cores = false ]]
2101                   then
2102                      catalog_option=""
2103                      catalog_string=""
2104                   else
2105                      catalog_option="-c"
2106                      catalog_string="/"
2107                   fi
2108                   append_option=""
2109                   append_string=""
2110                else
2111                   append_option="-A"
2112                   append_string="append"
2113                fi
2114
2115                transfer_failed=false
2116                printf "\n  >>> OUTPUT: ${localout[$i]}$catalog_string  $append_string by SCP to"
2117                printf "\n              ${pathout[$i]}/${host_configuration}_${fname}${endout[$i]}$catalog_string\n"
2118
2119                   # TRANSFER VIA SCP
2120                if [[ "$remote_loginnode" != "" ]]
2121                then
2122                   echo "cd $TEMPDIR; ${fast_io_catalog}/${sources_for_run_catalog}/batch_scp $PORTOPT $catalog_option $append_option -b -m $usecycle_option -u $local_username $return_address  ${localout[$i]} \"${pathout[$i]}\" ${host_configuration}_${fname}${endout[$i]}  ${extout[$i]}"  |  ssh -q $remote_username@$remote_loginnode
2123                else
2124                   batch_scp $PORTOPT $catalog_option $append_option -b -m $usecycle_option -u $local_username $return_address  ${localout[$i]} "${pathout[$i]}" ${host_configuration}_${fname}${endout[$i]}  ${extout[$i]}
2125                fi
2126                [[ $? != 0 ]]  &&  transfer_failed=true
2127
2128
2129                   # IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
2130                if [[ $transfer_failed = true ]]
2131                then
2132                   printf "  +++ transfer failed. Trying to save a copy on this host under:\n"
2133                   printf "      ${pathout[$i]}/${host_configuration}_${fname}${endout[$i]}_$run_id\n"
2134
2135                      # FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
2136                   eval  local_catalog=${pathout[$i]}
2137                   if [[ ! -d $local_catalog ]]
2138                   then
2139                      printf "  *** local directory does not exist. Trying to create:\n"
2140                      printf "      $local_catalog \n"
2141                      mkdir -p  $local_catalog
2142                   fi
2143                   eval  cp  ${localout[$i]}  ${pathout[$i]}/${host_configuration}_${fname}${endout[$i]}_$run_id
2144                   transfer_problems=true
2145                fi
2146
2147             else
2148
2149                   # UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST
2150                   # BE COPIED OR APPENDED ON THIS MACHINE
2151                if [[ "${actionout[$i]}" = tr ]]
2152                then
2153                   actionout[$i]=""
2154                else
2155                   actionout[$i]="a"
2156                fi
2157             fi
2158          fi
2159
2160
2161             # APPEND ON THIS MACHINE
2162          if [[ "${actionout[$i]}" = "a" ]]
2163          then
2164             if [[ "${extout[$i]}" != " "  &&  "${extout[$i]}" != "" ]]
2165             then
2166                printf "\n  >>> OUTPUT: ${localout[$i]}  append to"
2167                printf "\n              ${pathout[$i]}.${extout[$i]}\n"
2168                cat  ${localout[$i]}  >>  ${pathout[$i]}.${extout[$i]}
2169             else
2170                printf "\n  >>> OUTPUT: ${localout[$i]}  append to"
2171                printf "\n              ${pathout[$i]}\n"
2172                cat  ${localout[$i]}  >>  ${pathout[$i]}
2173             fi
2174          fi
2175
2176             # COPY ON THIS MACHINE
2177             # COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
2178             # ON DIFFERENT FILE-SYSTEMS
2179          if [[ "${actionout[$i]}" = ""  &&  $files_for_cores = false ]]
2180          then
2181
2182                # COPY IN CASE OF RUNS ON SINGLE CORES
2183             if [[ "${extout[$i]}" != " "  &&  "${extout[$i]}" != "" ]]
2184             then
2185                printf "\n  >>> OUTPUT: ${localout[$i]}  to"
2186                printf "\n              ${pathout[$i]}.${extout[$i]}\n"
2187                              if [[ $link_local_output = true ]]
2188                              then
2189                                 printf "      file will be linked\n"
2190                                 ln -f  ${localout[$i]}  ${pathout[$i]}.${extout[$i]}
2191                              fi
2192                                 # If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
2193                              if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
2194                then
2195                                 if [[ $link_local_output = true ]]
2196                          then
2197                      printf "  --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2198                                 fi
2199                                 cp  ${localout[$i]}  ${pathout[$i]}.${extout[$i]}
2200                              else
2201                   printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
2202                fi
2203             else
2204                printf "\n  >>> OUTPUT: ${localout[$i]}  to"
2205                printf "\n              ${pathout[$i]}\n"
2206                              if [[ $link_local_output = true ]]
2207                              then
2208                                 printf "      file will be linked\n"
2209                                 ln -f  ${localout[$i]}  ${pathout[$i]}
2210                              fi
2211                                 # If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
2212                        if [[ ! -f "${pathout[$i]}" ]]
2213                then
2214                                 if [[ $link_local_output = true ]]
2215                          then
2216                      printf "  --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2217                                 fi
2218                                 cp  ${localout[$i]}  ${pathout[$i]}
2219                              else
2220                                 printf "+++ no copy because file ${pathout[$i]} exists\n"
2221                fi
2222             fi
2223
2224          elif [[ "${actionout[$i]}" = ""  &&  $files_for_cores = true ]]
2225          then
2226
2227                # FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
2228                # AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
2229             printf "\n  >>> OUTPUT: ${localout[$i]}/_....  to"
2230             printf "\n              ${pathout[$i]}\n"
2231                    if [[ $link_local_output = true ]]
2232                    then
2233                              printf "      files will be linked\n"
2234                              mkdir -p ${pathout[$i]}
2235                              cd ${localout[$i]}
2236                              for file in $(ls *)
2237                              do
2238                                 ln -f $file  ${pathout[$i]}
2239                              done >|/dev/null 2>&1
2240                              cd $TEMPDIR
2241                    fi
2242
2243                # IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
2244                    if [[ ! -f "${pathout[$i]}/_000000" ]]
2245             then
2246                              if [[ $link_local_output = true ]]
2247                              then
2248                   printf "  --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2249                              fi
2250                              cp -r  ${localout[$i]}/*  ${pathout[$i]}
2251             fi
2252
2253          fi
2254       fi
2255    done
2256
2257    if (( i != 0 ))
2258    then
2259       if [[ $transfer_problems = true ]]
2260       then
2261          printf "\n$dashes\n  *** OUTPUT-files saved"
2262          printf "\n  +++ WARNING: some data transfers failed! \n"
2263       else
2264          printf "\n$dashes\n  *** all OUTPUT-files saved \n"
2265       fi
2266    fi
2267
2268
2269       # IF REQUIRED, START A RESTART-JOB
2270       # FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
2271    if [[ -f CONTINUE_RUN ]]
2272    then
2273
2274          # ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY):
2275          # -C TELLS PALMRUN THAT IT IS A RESTART-RUN
2276          # -v SILENT MODE WITHOUT INTERACTIVE QUERIES
2277          # -b START A BATCH JOB
2278       [[ $(echo $prc | grep -c "\-C") = 0 ]]  &&  prc="$prc -C"
2279       [[ $(echo $prc | grep -c "\-v") = 0 ]]  &&  prc="$prc -v"
2280       [[ $(echo $prc | grep -c "\-b") = 0 ]]  &&  prc="$prc -b"
2281
2282
2283          # REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
2284          # SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN
2285       if [[ $(echo $prc | grep -c "#") != 0 ]]
2286       then
2287          prc=`echo $prc | sed 's/#/r/g'`
2288       fi
2289
2290
2291          # START THE RESTART-JOB
2292       printf "\n\n  *** initiating restart-run on \"$local_ip\" using command:\n"
2293       echo "      $prc"
2294       printf "\n$dashes\n"
2295       if [[ $running_on_remote = true ]]
2296       then
2297
2298          echo "*** ssh will be used to initiate restart-runs!"
2299          echo "    return_address=\"$return_address\" "
2300          echo "    return_username=\"$local_username\" "
2301
2302          if [[ "$remote_loginnode" != "" ]]
2303          then
2304             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
2305          else
2306             echo \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" |  ssh -q $SSH_PORTOPT  $local_username@$return_address
2307          fi
2308
2309             # WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
2310          sleep 30
2311
2312       else
2313
2314             # START THE RESTART JOB ON THE LOCAL HOST
2315          eval  $prc                # THE ' MUST BE EVALUATED
2316          cd -  > /dev/null
2317
2318       fi
2319       printf "\n$dashes\n  *** restart-run initiated \n"
2320
2321
2322          # DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
2323          # DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
2324          # THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
2325          # MAY BE VERY HUGE)
2326       (( i = 0 ))
2327       while (( i < iin ))
2328       do
2329          (( i = i + 1 ))
2330          if [[ "${got_tmp[$i]}" = true   &&  $keep_data_from_previous_run = false ]]
2331          then
2332             rm -r  ${absnamein[$i]}
2333          fi
2334       done
2335
2336    fi
2337
2338
2339       # ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
2340    cd  $HOME
2341    [[ $delete_temporary_catalog = true ]]  &&  rm -rf $TEMPDIR
2342
2343
2344 else
2345
2346
2347       # PREPARING ACTIONS,
2348       # IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE
2349
2350       # BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB
2351    palmrun_com="$palmrun_script_name -d $fname -h $host_configuration -m $memory -t $cpumax -q $queue -r $run_id -U $local_username"
2352    [[ "$activation_string_list" != "" ]]  &&  palmrun_com=${palmrun_com}" -a \"$activation_string_list\""
2353    [[ "$global_revision" != "" ]]  &&  palmrun_com=${palmrun_com}" -G \"$global_revision\""
2354    [[ $keep_data_from_previous_run = true ]]  &&  palmrun_com=${palmrun_com}" -k"
2355    [[ $do_trace = true ]]        &&  palmrun_com=${palmrun_com}" -x"
2356    [[ "$cores" != "" ]]       &&  palmrun_com=${palmrun_com}" -X $cores"
2357    [[ $use_openmp = true ]]  &&  palmrun_com=${palmrun_com}" -O $threads_per_task"
2358    [[ $tasks_per_node != 0 ]]  &&  palmrun_com=${palmrun_com}" -T $tasks_per_node"
2359    [[ $delete_temporary_catalog = false ]]  &&  palmrun_com=${palmrun_com}" -B"
2360    [[ "$ocean_file_appendix" = true ]]  &&  palmrun_com=${palmrun_com}" -y"
2361    [[ $run_coupled_model = true ]]  &&  palmrun_com=${palmrun_com}" -Y \"$coupled_dist\""
2362    [[ "$combine_plot_fields" = false ]]  &&  palmrun_com=${palmrun_com}" -Z"
2363    [[ "$max_par_io_str" != "" ]]  &&  palmrun_com=${palmrun_com}" -w $max_par_io_str"
2364    [[ "$project_account" != "" ]]  &&  palmrun_com=${palmrun_com}" -A $project_account"
2365    if [[ $create_remote_batch_job = true ]]
2366    then
2367       palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip"
2368       if [[ $do_trace = true ]]
2369       then
2370          printf "\n *** PALMRUN-command on remote host:\n     $palmrun_com \n"
2371       fi
2372    elif [[ $create_batch_job = true ]]
2373    then
2374       palmrun_com=${palmrun_com}" -j"
2375       if [[ $do_trace = true ]]
2376       then
2377          printf "\n *** PALMRUN-command on local host:\n     $palmrun_com \n"
2378       fi
2379    fi
2380
2381
2382       # DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND
2383       # REMOTE HOST
2384    job_protocol_file_local=${local_jobcatalog}/${host_configuration}_${job_id}
2385    job_protocol_file=$job_protocol_file_local
2386    if [[ $create_remote_batch_job = true ]]
2387    then
2388       job_protocol_file_remote=${remote_jobcatalog}/${host_configuration}_${job_id}
2389       job_protocol_file=$job_protocol_file_remote
2390       job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol
2391       scpjob_file=${remote_jobcatalog}/scpjob.$run_id
2392    fi
2393
2394
2395       # BUILD THE JOB-SCRIPTS ON FILE jobfile
2396    jobfile=jobfile.$run_id
2397
2398
2399       # FIRST CREATE THE BATCH DIRECTIVES
2400    (( i = 0 ))
2401    while (( i < ibd ))
2402    do
2403       (( i = i + 1 ))
2404       line=`echo  "${batch_directive[$i]}" | sed 's/{{JOB_ID}}/$job_id/g' | sed 's/{{JOBFILE}}/$job_protocol_file/g' | sed 's/{{CPU_HOURS}}/$cpu_hours/g' | sed 's/{{CPU_MINUTES}}/$cpu_minutes/g' | sed 's/{{CPU_SECONDS}}/$cpu_seconds/g' | sed 's/{{NODES}}/$nodes/g' | sed 's/{{CORES}}/$cores/g' | sed 's/{{TASKS_PER_NODE}}/$tasks_per_node/g' | sed 's/{{HOST_CONFIGURATION}}/${host_configuration}/g' | sed 's/{{FNAME}}/$fname/g' | sed 's/{{QUEUE}}/$queue/g' | sed 's/{{MEMORY}}/$memory/g' | sed 's/{{PROJECT_ACCOUNT}}/$project_account/g' | sed 's/{{PREVIOUS_JOB}}/$previous_job/g'`
2405       eval line=\"$line\"
2406       echo  "$line"                               >>  $jobfile
2407    done
2408    echo " "                                       >>  $jobfile
2409
2410
2411       # FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB
2412       # PROTOCOL
2413    if [[ $create_remote_batch_job = true ]]
2414    then
2415       echo "set +vx"                              >>  $jobfile
2416       echo "trap '"                               >>  $jobfile
2417       echo "set +vx"                              >>  $jobfile
2418       echo "cd ${remote_jobcatalog}"              >>  $jobfile
2419       echo "cat >  scpjob.$run_id << %%END%%"     >>  $jobfile
2420
2421          # ADD THE BATCH DIRECTIVES
2422       (( i = 0 ))
2423       while (( i < ibdt ))
2424       do
2425          (( i = i + 1 ))
2426          line=`echo  "${batch_directive_transfer[$i]}" | sed 's/{{JOB_ID}}/$job_id/g' | sed 's/{{JOBFILE}}/$job_protocol_file/g' | sed 's/{{JOB_TRANSFER_PROTOCOL_FILE}}/$job_transfer_protocol_file/g' | sed 's/{{CPU_HOURS}}/$cpu_hours/g' | sed 's/{{CPU_MINUTES}}/$cpu_minutes/g' | sed 's/{{CPU_SECONDS}}/$cpu_seconds/g' | sed 's/{{NODES}}/$nodes/g' | sed 's/{{TASKS_PER_NODE}}/$tasks_per_node/g' | sed 's/{{HOST_CONFIGURATION}}/${host_configuration}/g' | sed 's/{{FNAME}}/$fname/g' | sed 's/{{PROJECT_ACCOUNT}}/$project_account/g'`
2427          eval line=\"$line\"
2428          echo  "$line"                            >>  $jobfile
2429       done
2430       echo " "                                    >>  $jobfile
2431
2432       echo "set -x"                               >>  $jobfile
2433       echo "${fast_io_catalog}/${sources_for_run_catalog}/batch_scp  $PORTOPT  -d  -w 10  -u $local_username $local_ip  $job_protocol_file_remote  \"$local_jobcatalog\"  ${host_configuration}_${fname}"  >>  $jobfile
2434       echo "%%END%%"                              >>  $jobfile
2435       echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" "  >>  $jobfile
2436       echo "$submit_command  $scpjob_file"        >>  $jobfile
2437       echo "rm $scpjob_file"                      >>  $jobfile
2438       echo "rm -rf $job_transfer_protocol_file"   >>  $jobfile
2439       echo "set -x"                               >>  $jobfile
2440       echo "     ' exit"                          >>  $jobfile
2441    fi
2442
2443
2444       # ACTIVATE ERROR-TRACEBACK
2445    if [[ $do_trace = true ]]
2446    then
2447       echo  "set -x"                                    >>  $jobfile
2448    else
2449       echo  "set +vx"                                   >>  $jobfile
2450    fi
2451
2452
2453       # INITIALIZE THE ENVIRONMENT AND LOAD MODULES
2454    if [[ "$login_init_cmd" != "" ]]
2455    then
2456       echo  "$login_init_cmd"        >>  $jobfile
2457    fi
2458    if [[ "$module_commands" != "" ]]
2459    then
2460       echo  "$module_commands"     >>  $jobfile
2461    fi
2462
2463
2464       # CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
2465    echo  "mkdir  $TEMPDIR"              >>  $jobfile
2466    echo  "cd  $TEMPDIR"                 >>  $jobfile
2467    echo  "export TEMPDIR=$TEMPDIR"      >>  $jobfile
2468    echo  "cp  ${fast_io_catalog}/${sources_for_run_catalog}/{*,.[!.]*}  ."  >>  $jobfile
2469    echo  "export PATH=.:\$PATH"         >>  $jobfile
2470    echo  "export execute_palmrun=true"  >>  $jobfile
2471
2472
2473       # GET REQUIRED INPUT-FILES BY SCP OR BY SENDING THEM WITH THE JOB AS HERE-DOCUMENT
2474       # PUT THESE FILES INTO THE USER'S RESPECTIVE PERMANENT DIRECTORIES ON THE REMOTE-HOST
2475       # IF THE DIRECTORIES DO NOT EXIST, TRY TO CREATE THEM
2476    if [[ $create_remote_batch_job = true ]]
2477    then
2478       (( i = 0 ))
2479       while (( i < iin ))
2480       do
2481          (( i = i + 1 ))
2482          echo  "[[ ! -d ${pathin[$i]} ]]  &&  mkdir -p  ${pathin[$i]}"  >>  $jobfile
2483          if [[ "${transin[$i]}" = job ]]
2484          then
2485             echo  "cat > ${remotepathin[$i]} <<\"%END%\""    >>  $jobfile
2486             eval cat   ${pathin[$i]}/${frelin[$i]}           >>  $jobfile
2487             echo  " "                                        >>  $jobfile
2488             echo  "%END%"                                    >>  $jobfile
2489          else
2490             echo  "batch_scp $PORTOPT -b -o -g -s -u $local_username $return_address ${remotepathin[$i]} \"${pathin[$i]}\" ${frelin[$i]}" >>  $jobfile
2491          fi
2492
2493             # CHECK, IF FILE COULD BE CREATED
2494          echo  "if [[ \$? = 1 ]]"                    >>  $jobfile
2495          echo  "then"                                >>  $jobfile
2496          echo  "   echo \" \" "                      >>  $jobfile
2497          echo  "   echo \"+++ file ${remotepathin[$i]} could not be created\" "   >>  $jobfile
2498          echo  "   echo \"    please check, if directory exists on $host_configuration!\" "  >>  $jobfile
2499          echo  "   echo \"+++ PALMRUN will not be continued\" "  >>  $jobfile
2500          echo  "   execute_palmrun=false"            >>  $jobfile
2501          echo  "fi"                                  >>  $jobfile
2502       done
2503    fi
2504
2505
2506       # PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
2507       # STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN
2508       # IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
2509    echo  "LOCAL_PWD=$working_directory"                >>  $jobfile
2510    echo  "export LOCAL_PWD"                            >>  $jobfile
2511
2512
2513       # PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON
2514    echo  "LOCAL_PALMRUN_PATH=${source_path}/../SCRIPTS"   >>  $jobfile
2515    echo  "export LOCAL_PALMRUN_PATH"                      >>  $jobfile
2516
2517
2518       # CALL PALMRUN WITHIN THE JOB
2519       # AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
2520    echo  "set -x"                                              >>  $jobfile
2521    echo  "[[ \$execute_palmrun = true ]]  &&  $palmrun_com"    >>  $jobfile
2522
2523
2524       # TRANSFER JOBFILE TO THE TARGET HOST
2525    if [[ $create_jobfile_only = false ]]
2526    then
2527
2528       if [[ $create_remote_batch_job = true ]]
2529       then
2530
2531          echo " "
2532          echo "  *** transfer of job to remote host via scp"
2533          if [[ $do_trace = true ]]
2534          then
2535             echo "     scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_configuration}_${job_id}"
2536          fi
2537          scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_configuration}_${job_id}
2538
2539          echo " "
2540          echo "  *** submit the job (output of submit command, e.g. the job-id, may follow)"
2541          if [[ $do_trace = true ]]
2542          then
2543             echo "     cd $remote_jobcatalog; $submit_command ${host_configuration}_${job_id}; rm ${host_configuration}_${job_id}  |  ssh  -q  $ssh_key $SSH_PORTOPT  ${remote_username}@${remote_ip}  2>&1"
2544          fi
2545          echo "cd $remote_jobcatalog; $submit_command ${host_configuration}_${job_id}; rm ${host_configuration}_${job_id}"  |  ssh  -q  $ssh_key $SSH_PORTOPT  ${remote_username}@${remote_ip}  2>&1
2546
2547       elif [[ $create_batch_job = true ]]
2548       then
2549
2550          eval  local_jobcatalog=$local_jobcatalog
2551          cp  $jobfile  ${local_jobcatalog}/${host_configuration}_${job_id}
2552          cd $local_jobcatalog
2553          echo " "
2554          echo " *** submit the job"
2555          if [[ $do_trace = true ]]
2556          then
2557             echo "$submit_command ${host_configuration}_${job_id}"
2558          fi
2559          $submit_command ${host_configuration}_${job_id}
2560          rm ${host_configuration}_${job_id}
2561          cd -  > /dev/null
2562
2563       fi
2564
2565       rm -rf  $jobfile
2566
2567    else
2568
2569       printf "\n *** jobfile created under name \"$jobfile\" "
2570       printf "\n     no batch-job has been sent!"
2571
2572    fi
2573
2574 fi  # END OF REMOTE-PART
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