source: palm/trunk/SCRIPTS/palmrun @ 3151

Last change on this file since 3151 was 3151, checked in by raasch, 3 years ago

output of PALM code revision number in palmrun header, some preprocessor define strings removed, small revisions in configuration files

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File size: 98.3 KB
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1#!/bin/bash
2
3# palmrun - script for running PALM jobs
4
5#--------------------------------------------------------------------------------#
6# This file is part of the PALM model system.
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 2017-2018  Leibniz Universitaet Hannover
20#--------------------------------------------------------------------------------#
21#
22# Current revisions:
23# ------------------
24#
25#
26# Former revisions:
27# -----------------
28# $Id: palmrun 3151 2018-07-19 08:45:38Z raasch $
29# removed additional listing of files to be compiled, print PALM code revision
30# in header
31#
32# 3132 2018-07-16 11:44:58Z raasch
33# create consistent error messages in case of failed restarts,
34# check existence of remote job catalog
35#
36# 3043 2018-05-25 10:47:54Z raasch
37# check for setting of fast_io_catalog
38#
39# 3033 2018-05-23 15:26:19Z raasch
40# -T option not required for interactive runs (tasks per node =
41# total number of cores is assumed as default, if option is not given),
42# reformatting of a few messages,
43# bugfix: destination output directory is created if attribute "pe" is set in
44# .palm.iofiles
45#
46# 2718 2018-01-02 08:49:38Z maronga
47# bugfix of r2990
48#
49# 2718 2018-01-02 08:49:38Z maronga
50# bugfix: temporary SOURCES_FOR_RUN_CATALOG now created in base_directory and
51#         not in the working directory from where palmrun is called
52#
53# 2718 2018-01-02 08:49:38Z maronga
54# svfout in the activation string will be replaced now by svfin in case of
55# automatic restarts
56#
57# 2718 2018-01-02 08:49:38Z maronga
58# Introduction of new ENVIRONMENT variables read_svf and write_svf to consider
59# the possible output or input of sky view factors
60#
61# 2718 2018-01-02 08:49:38Z maronga
62# "fname" renamed to "jobname"
63#
64# 2718 2018-01-02 08:49:38Z maronga
65# parameters are allowed in output commands (OC:)
66#
67# 2718 2018-01-02 08:49:38Z maronga
68# bugfix: exit if no queue has been given neither with option -q nor in the
69# configuration file
70#
71# 2718 2018-01-02 08:49:38Z maronga
72# file connection file from trunk/SCRIPTS is taken by default
73#
74# 2718 2018-01-02 08:49:38Z maronga
75# Corrected "Former revisions" section
76#
77# 2696 2017-12-14 17:12:51Z kanani
78# Change in file header (GPL part)
79#
80# 2693 2017-12-13 12:33:49Z raasch
81# replacement of variables given by {{<variable>}} in configuration file is now
82# done in a more general way, variable names are written in small letters
83#
84# 2670 2017-12-06 16:32:19Z raasch
85# test printouts removed
86#
87# 2669 2017-12-06 16:03:27Z raasch
88# file attributes in .palm.iofiles restructured, "loc" attribute completely
89# removed,
90# wildcard (*) allowed in .palm.iofiles as file activation string for output
91# files,
92# informative messages in case of missing optional input files shortened
93# bugfix: variable cycle explicitly interpreted with 10 as the number base
94#
95# 2638 2017-11-23 12:44:23Z raasch
96# use of wildcards in file connection statements enabled
97#
98# 2605 2017-11-09 15:31:46Z raasch
99# in case of remote jobs, input files with "job" or "jobopt" (new) attribute
100# will not be sent with the job file any more, but copied into the
101# SOURCES_FOR_RUN... folder on the remote host, before the job is submitted
102#
103# 2600 2017-11-01 14:11:20Z raasch
104# cycle numbers are made three digits wide
105#
106# 2566 2017-10-20 08:50:47Z raasch
107# execute command for combine_plot_fields added
108# "TEMPDIR" renamed "tempdir"
109# temporary working directory for local batch jobs is created immediately within
110# the user's palmrun call, due to a requirement of the "grid engine" batch
111# system, where the working directory is given with batch directive -wd and must
112# already exist when the job is submitted,
113# informative messages in non-trace mode reduced and partly reformatted
114#
115# 2551 2017-10-18 07:25:11Z raasch
116# TEMPDIR added as replacement string to be used in batch directives
117#
118# 2512 2017-10-04 08:26:59Z raasch
119# bugfix for determining cycle numbers of NetCDF input files
120#
121# 2506 2017-09-29 08:30:37Z raasch
122# option -V added to check for an existing SOURCES_FOR_RUN_... folder
123# host configuration added to SOURCES_FOR_RUN_... folder name
124# host_identifier renamed host_configuration
125# option -W added to allow for job dependencies
126#
127# 2501 2017-09-26 11:41:55Z raasch
128# default value for number of cores (option -X) set to 1
129# bugfix for mechanism which overwrites configuration file settings with values
130# provided by palmrun options
131#
132# 2499 2017-09-22 16:47:58Z kanani
133# option -h named configuration identifier
134#
135# 2480 2017-09-19 06:24:14Z maronga
136# bugfix for last revision
137#
138# 2479 2017-09-19 06:12:16Z raasch
139# option -A (project account number) added
140#
141# 2422 2017-09-08 08:25:41Z raasch
142# initial revision
143#
144#--------------------------------------------------------------------------------#
145# palmrun - script for running PALM jobs on local and remote hosts
146#--------------------------------------------------------------------------------#
147
148
149 
150    # DECLARATION OF VARIABLES AND THEIR DEFAULT VALUES
151
152 set +o allexport    # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
153                     # LEAD TO PROBLEMS IN ROUTINES CALLED BY PALMRUN
154                     # (TOO MANY ARGUMENTS - PROBLEM)
155 set +o noclobber    # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
156
157 typeset -i  ibd=0 ibdt=0 iec=0 iic=0 iin=0 ioc=0 iout=0 nr_of_input_files=0
158 typeset -i  nr_of_output_files=0
159 typeset -x -i  memory=0   # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
160                           # SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
161                           # SCRIPT-OPTION ARGUMENTS
162 typeset -i  cores cputime cpu_hours cpu_minutes cpu_seconds i ii iia iii iio
163 typeset -i  icycle inode ival maxcycle mpi_tasks
164 typeset -i  nodes remaining_cores run_number tasks_per_node threads_per_task
165
166 activation_string_list=""
167 AddFilenames=""
168 combine_plot_fields=true
169 compiler_name=""
170 compiler_name_ser=""
171 compiler_options=""
172 cores=1
173 cores_atmos=0
174 cores_ocean=0
175 coupled_dist=""
176 cpp_options=""
177 cpumax=0
178 create_batch_job=false
179 create_jobfile_only=false
180 create_remote_batch_job=false
181 dashes="  ----------------------------------------------------------------------------"
182 defaultqueue=""
183 delete_temporary_catalog=true
184 do_compile=true
185 do_trace=false
186 executable=""
187 execute_command=""
188 execution_error=false
189 fileconnection_file=trunk/SCRIPTS/.palm.iofiles
190 jobname=test
191 global_revision=""
192 host_configuration="default"
193 hostfile=""
194 hp=""
195 keep_data_from_previous_run=false
196 link_local_input=false
197 link_local_output=false
198 linker_options=""
199 local_jobcatalog=""
200 locat=normal
201 makefile=""
202 max_par_io_str=""
203 prc=$0
204 while [[ $(echo $prc | grep -c "/") != 0 ]]
205 do
206    prc=`echo $prc | cut -f2- -d"/"`
207 done
208 module_calls=""
209 palmrun_memory=""
210 palmrun_script_name=$prc
211 openmp=false
212 previous_job=""
213 project_account=""
214 queue=none
215 read_svf=""
216 restart_run=false
217 return_address=""
218 remote_jobcatalog=""
219 remote_username=""
220 running_in_batch_mode=false
221 run_coupled_model=false
222 run_id=""
223 silent=false
224 source_list=""
225 source_path=""
226 tasks_per_node=0
227 threads_per_task=1
228 transfer_problems=false
229 user_source_path=""
230 use_existing_sources_folder=""
231 use_openmp=false
232 version="palmrun  1.0 Rev$Rev: 3151 $"
233 working_directory=`pwd`
234 write_binary=""
235 write_svf=""
236
237
238    # ERROR HANDLING IN CASE OF EXIT
239 trap 'if [[ $locat != normal  &&  $locat != control_c ]]
240       then
241
242              # CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
243          (( i = 0 ))
244          while (( i < iec ))
245          do
246             (( i = i + 1 ))
247             printf "\n  *** Execution of ERROR-command:\n"
248             printf "  >>> ${err_command[$i]}\n"
249             eval  ${err_command[$i]}
250          done
251          [[ $delete_temporary_catalog = true ]]  &&  (cd; rm -rf $tempdir)
252          printf "\n\n+++ palmrun killed \n\n"
253       elif [[ $locat != control_c ]]
254       then
255          printf "\n --> palmrun finished\n\n"
256       fi' exit
257
258
259    # ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
260 trap 'cd; rm -rf $tempdir
261       printf "\n+++ palmrun killed by \"^C\" \n\n"
262       locat=control_c
263       exit
264      ' 2
265
266
267    # READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc),
268    # WHICH WILL BE USED TO START RESTART-JOBS
269 while  getopts  :a:A:bBCd:FG:h:jkm:M:O:q:r:R:s:t:T:u:U:vVw:W:xX:yY:Z option
270 do
271   case  $option  in
272       (a)   activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";;
273       (A)   project_account=$OPTARG; prc="$prc -A'$OPTARG'";;
274       (b)   create_batch_job=true; prc="$prc -b";;
275       (B)   delete_temporary_catalog=false; prc="$prc -B";;
276       (C)   restart_run=true; prc="$prc -C";;
277       (d)   jobname=$OPTARG; prc="$prc -d$OPTARG";;
278       (F)   create_jobfile_only=true;;
279       (G)   global_revision=$OPTARG; prc="$prc -G'$OPTARG'";;
280       (h)   host_configuration=$OPTARG; prc="$prc -h$OPTARG";;
281       (j)   running_in_batch_mode=true;;
282       (k)   keep_data_from_previous_run=true; prc="$prc -k";;
283       (m)   palmrun_memory=$OPTARG; prc="$prc -m$OPTARG";;
284       (M)   makefile=$OPTARG; prc="$prc -M$OPTARG";;
285       (O)   use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";;
286       (q)   queue=$OPTARG; prc="$prc -q$OPTARG";;
287       (r)   run_id=$OPTARG;;
288       (R)   return_address=$OPTARG;;
289       (s)   source_list=$OPTARG;;
290       (t)   palmrun_cpumax=$OPTARG; prc="$prc -t$OPTARG";;
291       (T)   palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";;
292       (u)   remote_username=$OPTARG; prc="$prc -u$OPTARG";;
293       (U)   return_username=$OPTARG; prc="$prc -U$OPTARG";;
294       (v)   silent=true; prc="$prc -v";;
295       (V)   use_existing_sources_folder="-V";;
296       (w)   max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";;
297       (W)   previous_job=$OPTARG;;
298       (x)   do_trace=true;set -x; prc="$prc -x";;
299       (X)   palmrun_cores=$OPTARG; prc="$prc -X$OPTARG";;
300       (y)   ocean_file_appendix=true; prc="$prc -y";;
301       (Y)   run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";;
302       (Z)   combine_plot_fields=false; prc="$prc -Z";;
303       (\?)  printf "\n  +++ unknown option $OPTARG \n"
304             printf "\n  --> type \"$0 ?\" for available options \n"
305             locat=parameter;exit;;
306   esac
307 done
308
309
310    # SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
311    # CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
312 (( to_shift = $OPTIND - 1 ))
313 shift $to_shift
314
315    # PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS
316 if [[ "$1" = "?" ]]
317 then
318   (printf "\n  *** Description of available palmrun options:\n"
319    printf "\n      Option  Description                              Default-Value"
320    printf "\n        -a    activation string list                   \"\" "
321    printf "\n        -A    project account number                   ---"
322    printf "\n        -b    batch-job on local machine               ---"
323    printf "\n        -B    do not delete temporary directory at end ---"
324    printf "\n        -d    run identifier                           test"
325    printf "\n        -F    create batch job file only               ---"
326    printf "\n        -h    host configuration                       \"default\" "
327    printf "\n        -k    keep data from previous run"
328    printf "\n        -m    memory demand in MB (batch-jobs)         0 MB"
329    printf "\n        -M    Makefile name                            Makefile"
330    printf "\n        -O    threads per openMP task                  ---"
331    printf "\n        -q    queue                                    \"$queue\" "
332    printf "\n        -s    filenames of routines to be compiled     \"\" "
333    printf "\n              must end with .f, .f90, .F, or .c !"
334    printf "\n              use \"..\" for more than one file and wildcards"
335    printf "\n              -s LM compiles all locally modified files"
336    printf "\n        -t    allowed cpu-time in seconds (batch)      0"
337    printf "\n        -T    tasks per node                           ---"
338    printf "\n        -u    username on remote machine               \"\" "
339    printf "\n        -v    no prompt for confirmation               ---"
340    printf "\n        -V    check if SOURCES_FOR_RUN_... exists      ---"
341    printf "\n        -w    maximum parallel io streams              as given by -X"
342    printf "\n        -W    name of job to wait for                  ---"
343    printf "\n        -x    tracing of palmrun for debug purposes    ---"
344    printf "\n        -X    # of processors (on parallel machines)   1"
345    printf "\n        -y    add appendix \"_O\" to all local output"
346    printf "\n              files (ocean precursor runs followed by"
347    printf "\n              coupled atmosphere-ocean runs)           ---"
348    printf "\n        -Y    run coupled model, \"#1 #2\" with" 
349    printf "\n              #1 atmosphere and #2 ocean processors    \"#/2 #/2\" depending on -X"
350    printf "\n        -Z    skip combine_plot_fields at the end of      "
351    printf "\n              the simulation                           ---"
352    printf "\n "
353    printf "\n      Possible values of positional parameter <modus>:"
354    printf "\n        \"?\"       -  this outline \n\n") | more
355    exit
356 elif [[ "$1" != "" ]]
357 then
358    printf "\n  +++ positional parameter $1 unknown \n"
359    locat=parameter; exit
360 fi
361
362
363
364    # SHORT STARTING MESSAGE
365 printf "\n*** $version "
366 printf "\n    will be executed.     Please wait ..."
367
368
369    # FOR COMPATIBILITY REASONS SET OLD ENVIRONMENT VARIABLE
370 export fname=$jobname
371
372
373    # BUILD THE CONFIGURATION-FILE NAME AND THE SOURCES_FOR_RUN-FOLDER NAME
374 config_file=.palm.config.$host_configuration
375 sources_for_run_catalog=SOURCES_FOR_RUN_${host_configuration}_$jobname
376
377
378    # CHECK, IF CONFIGURATION FILE EXISTS
379 if [[ ! -f $config_file ]]
380 then
381    printf "\n\n  +++ configuration file: "
382    printf "\n           $config_file"
383    printf "\n      does not exist"
384    locat=connect; exit 
385 fi
386
387
388    # CHECK, IF USER PROVIDES OWN FILE CONNECTION FILE
389 if [[ -f .palm.iofiles ]]
390 then
391    fileconnection_file=.palm.iofiles
392 fi
393
394
395    # CHECK, IF FILE CONNECTION FILE EXISTS
396 if [[ ! -f $fileconnection_file ]]
397 then
398    printf "\n\n  +++ file connection file: "
399    printf "\n           $fileconnection_file"
400    printf "\n      does not exist"
401    locat=connect; exit 
402 fi
403
404
405    # CHECK, IF THE ACTIVATION_STRING_LIST HAS BEEN GIVEN
406 if [[ "$activation_string_list" = "" ]]
407 then
408    printf "\n\n  +++ no activation string list given: "
409    printf "\n        please set palmrun option \"-a\" "
410    locat=palmrun_option; exit 
411 fi
412
413
414    # SET VARIABLE TO ACTIVATE PALM BINARY OUTPUT FOR RESTARTS
415 if [[ $(echo $activation_string_list | grep -c "restart") != 0 ]]
416 then
417    write_binary=true
418 else
419    write_binary=false
420 fi
421
422    # SET VARIABLE TO ACTIVATE WRITING OF SVF DATA
423 if [[ $(echo $activation_string_list | grep -c "svfout") != 0 ]]
424 then
425    write_svf=true
426 else
427    write_svf=false
428 fi
429
430    # SET VARIABLE TO ACTIVATE READING OF SVF DATA
431 if [[ $(echo $activation_string_list | grep -c "svfin") != 0 ]]
432 then
433    read_svf=true
434 else
435    read_svf=false
436 fi
437
438
439    # READ AND EVALUATE THE CONFIGURATION-FILE
440 [[ $silent = false ]]  &&  printf "\n\n    Reading the configuration file... "
441
442    # READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE
443 while  read line
444 do
445
446       # FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
447    eval  line=\"$line\"
448
449
450       # INTERPRET THE LINE
451    if [[ "$(echo $line)" = "" ]]
452    then
453
454          # EMPTY LINE, NO ACTION
455       continue
456
457    elif [[ "$(echo $line | cut -c1)"  =  "#" ]]
458    then
459
460          # LINE IS A COMMENT LINE
461       continue
462
463    elif [[ "$(echo $line | cut -c1)"  =  "%" ]]
464    then
465
466          # LINE DEFINES AN ENVIRONMENT-VARIABLE
467       var=`echo $line | cut -d" " -s -f1 | cut -c2-`
468       value=`echo $line | cut -d" " -s -f2-`
469
470
471          # VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
472          # ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
473          # ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
474          # NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
475          # HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
476          # CONFIGURATION-FILE.
477       if [[ "$(eval echo \$$var)" = ""  ||  "$(eval echo \$$var)" = "0" ]]
478       then
479          eval  export  $var="\$value"
480
481             # TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
482          if [[ $do_trace = true ]]
483          then
484             printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
485          fi
486       fi
487
488    elif [[ "$(echo $line | cut -c1-3)" = "BD:" ]]
489    then
490
491          # LINE DEFINES BATCH-DIRECTIVE
492       (( ibd = ibd + 1 ))
493       line=$(echo $line | cut -c4-)
494       batch_directive[$ibd]="$line"
495
496    elif [[ "$(echo $line | cut -c1-4)" = "BDT:" ]]
497    then
498
499          # LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A
500          # REMOTE TO A LOCAL HOST
501       (( ibdt = ibdt + 1 ))
502       line=$(echo $line | cut -c5-)
503       batch_directive_transfer[$ibdt]="$line"
504
505    elif [[ "$(echo $line | cut -c1-3)" = "EC:" ]]
506    then
507
508          # LINE DEFINES ERROR-COMMAND
509       (( iec = iec + 1 ))
510       line=$(echo $line | cut -c4-)
511       err_command[$iec]="$line"
512
513    elif [[ "$(echo $line | cut -c1-3)" = "IC:" ]]
514    then
515
516          # LINE DEFINES INPUT-COMMAND
517       (( iic = iic + 1 ))
518       line=$(echo $line | cut -c4-)
519       in_command[$iic]="$line"
520
521    elif [[ "$(echo $line | cut -c1-3)" = "OC:" ]]
522    then
523
524          # LINE DEFINES OUTPUT-COMMAND
525       (( ioc = ioc + 1 ))
526       line=$(echo $line | cut -c4-)
527       out_command[$ioc]="$line"
528
529    else
530
531          # SKIP ALL OTHER LINES
532       continue
533
534    fi
535
536 done < $config_file
537
538
539    # CHECK SETTING OF REQUIRED PARAMETERS
540 if [[ "$fast_io_catalog" = "" ]]
541 then
542    printf "\n  +++ no fast_io_catalog found in $config_file"
543    printf "\n      Please add line \"fast_io_catalog ...\" to that file."
544    locat=config_file; exit
545 fi
546 if [[ "$compiler_name" = "" ]]
547 then
548    printf "\n  +++ no compiler name found in $config_file"
549    printf "\n      Please add line \"compiler_name ...\" to that file."
550    locat=config_file; exit
551 fi
552 if [[ "$compiler_name_ser" = "" ]]
553 then
554    printf "\n  +++ no compiler name for non-paralle compilation found in $config_file"
555    printf "\n      Please add line \"compiler_name_ser ...\" to that file."
556    locat=config_file; exit
557 fi
558 if [[ "$compiler_options" = "" ]]
559 then
560    printf "\n  +++ no compiler options found in $config_file"
561    printf "\n      Please add line \"compiler_options ...\" to that file."
562    locat=config_file; exit
563 fi
564 if [[ "$linker_options" = "" ]]
565 then
566    printf "\n  +++ no linker options found in $config_file"
567    printf "\n      Please add line \"linker_options ...\" to that file."
568    locat=config_file; exit
569 fi
570 if [[ "$execute_command" = "" ]]
571 then
572    printf "\n  +++ no execute command found in $config_file"
573    printf "\n      Please add line \"execute_command ...\" to that file."
574    locat=config_file; exit
575 fi
576
577 if [[ "$hostfile" != "" ]]
578 then
579    if [[ $hostfile != auto  &&  ! -f $hostfile ]]
580    then
581       printf "\n  +++ no hostfile \"$hostfile\" found"
582       printf "\n      Please check line \"hostfile ...\" in $config_file"
583       locat=config_file; exit   
584    fi
585 fi
586
587
588    # DETERMINE THE CALL STATUS
589 if [[ "$return_address" != "" ]]
590 then
591 
592       # I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN
593       # BATCH MODE AND ...
594    running_on_remote=true
595 
596 else
597
598       # I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST
599     if [[ "$remote_ip" != "" ]]
600     then
601
602           # I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST
603        create_remote_batch_job=true
604
605           # CHECK THAT THE REMOTE JOBCATALOG HAS BEEN SET
606        if [[ "$remote_jobcatalog" = "" ]]
607        then
608           printf "\n  +++ no remote jobcatalog found in $config_file"
609           printf "\n      Please add line \"remote_jobcatalog ...\" to that file."
610           locat=config_file; exit
611        fi
612 
613
614     fi
615     running_on_remote=false
616 fi
617
618
619
620    # READ AND EVALUATE THE I/O-FILE LIST
621 [[ $silent = false ]]  &&  printf "\n    Reading the I/O files... "
622
623    # READ THE FILE CONNECTION FILE LINE BY LINE
624 while  read line
625 do
626
627       # REPLACE REPEATING SPACES BETWEEN THE COLUMNS BY A SINGLE SPACE
628    line=`echo "$line" | sed -e "s/\s\{1,\}/ /g"`
629
630       # INTERPRET THE LINE
631    if [[ "$(echo $line)" = "" ]]
632    then
633          # EMPTY LINE, NO ACTION
634       continue
635
636    elif [[ "$(echo $line | cut -c1)"  =  "#" ]]
637    then
638
639          # LINE IS A COMMENT LINE
640       true
641
642    else
643
644          # LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
645          # s2a: in/out - field
646          # s2b: action - field (optional)
647       s1=`echo "$line" | cut -d" " -f1`
648       s2=`echo "$line" | cut -d" " -s -f2`
649       if [[ $(echo $s2 | grep -c ":") = 0 ]]
650       then
651          s2a=$s2
652          s2b=""
653       else
654          s2a=`echo $s2 | cut -d":" -f1`
655          s2b=`echo $s2 | cut -d":" -f2`
656       fi
657       s3=`echo "$line" | cut -d" " -f3 | sed 's/*/wildcard /g'`
658       s4=`echo "$line" | cut -d" " -s -f4`
659       eval s4=\"$s4\"    # REPLACE ENVIRONMENT-VARIABLES IN PATH BY THEIR RESPECTIVE VALUES
660       s5=`echo "$line" | cut -d" " -s -f5`
661       s6=`echo "$line" | cut -d" " -s -f6`
662
663       
664          # STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
665          # INPUT- OR OUTPUT-LIST.
666          # VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
667          # IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
668          # LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b != tr), THE FILE CONNECTION
669          # IS NOT CHECKED AND STORED.
670       IFSALT="$IFS"; IFS="$IFS:"      # ADD ":" AS FIELD SEPARATOR
671       if [[ ( "$s2a" = in  || "$s2a" = inopt )  &&  ! ( $create_remote_batch_job = true  &&  "$s2b" != tr ) ]]
672       then
673          found=false
674          for  actual  in  $activation_string_list
675          do
676             for  formal  in  $s3
677             do
678                [[ $actual = $formal  ||  "$formal" = "-" ]]  &&  found=true
679             done
680          done
681          if [[ $found = true ]]
682          then
683             (( iin = iin + 1 ))
684             localin_pre[$iin]=$s1; actionin_pre[$iin]=$s2b;
685             pathin_pre[$iin]=$s4; endin_pre[$iin]=$s5; extin_pre[$iin]=$s6
686             if [[ "$s2a" = inopt ]]
687             then
688                optin_pre[$iin]=yes
689             else
690                optin_pre[$iin]=no
691             fi 
692
693                # FILES WITH JOB-ATTRIBUTE ARE STORED IN THE SOURCES_FOR_RUN
694                # FOLDER IF THE JOB IS RUNNING ON A REMOTE HOST
695             if [[ $running_on_remote = true  &&  "$s2b" = tr ]]
696             then
697                pathin_pre[$iin]=${fast_io_catalog}/${sources_for_run_catalog}
698             fi
699
700                # CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
701                # THE WILDCARD FROM THE ENDING
702             if [[ "${s5: -1}" = "*" ]]
703             then
704                if [[ "$s2b" = "di" ]]
705                then
706                   printf "\n    +++ wildcards (*) not allowed with \"di\" file attribute."
707                   printf "\n        see file \"$fileconnection_file\", line"
708                   printf "\n$line"
709                   locat=iofiles_file; exit
710                fi
711                multin[$iin]=true
712                string=${endin_pre[$iin]}
713                endin_pre[$iin]="${string%?}"
714             else
715                multin[$iin]=false
716             fi
717          fi
718       elif [[ "$s2a" = out  &&  ! ( $create_remote_batch_job = true ) ]]
719       then
720          found=false
721          for  actual  in  $activation_string_list
722          do
723             for  formal  in  $s3 
724             do
725                [[ $actual = $formal  ||  $formal = wildcard  ]]  &&  found=true
726             done
727          done
728          if [[ $found = true ]]
729          then
730             (( iout = iout + 1 ))
731             localout_pre[$iout]=$s1; actionout_pre[$iout]=$s2b
732             pathout_pre[$iout]=$s4; endout_pre[$iout]=$s5; extout_pre[$iout]=$s6
733
734                # CHECK IF WILDCARD IS USED AS ACTIVATION STRING
735                # IN SUCH CASES, NO WARNING WILL LATER BE OUTPUT IF LOCAL FILES DO NOT EXIST
736             if [[ $formal = wildcard  ]]
737             then
738                warnout_pre[$iout]=false
739             else
740                warnout_pre[$iout]=true
741             fi
742
743                # CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
744                # THE WILDCARD FROM THE LOCAL FILENAME
745             if [[ "${s1: -1}" = "*" ]]
746             then
747                if [[ "$s2b" = "di" ]]
748                then
749                   printf "\n    +++ wildcards (*) not allowed with \"di\" file attribute."
750                   printf "\n        see file \"$fileconnection_file\", line"
751                   printf "\n$line"
752                   locat=iofiles_file; exit
753                fi
754                multout[$iout]=true
755                string=${localout_pre[$iout]}
756                localout_pre[$iout]="${string%?}"
757             else
758                multout[$iout]=false
759             fi
760          fi
761       elif [[ "$s2a" != in  &&  "$s2a" != inopt  &&  "$s2a" != out ]]
762       then
763          printf "\n  +++ I/O-attribute in file $fileconnection_file has invalid"
764          printf "\n      value \"$s2\". Only \"in\", \"inopt\", and \"out\" are allowed!"
765          locat=connect; exit
766       fi
767       IFS="$IFSALT"
768    fi
769
770 done < $fileconnection_file
771
772
773
774    # VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
775 [[ "$palmrun_memory" != "" ]]  &&  memory=$palmrun_memory
776 [[ "$palmrun_cpumax" != "" ]]  &&  cpumax=$palmrun_cpumax
777 [[ "$palmrun_cores"  != "" ]]  &&  cores=$palmrun_cores
778 [[ "$max_par_io_str" != "" ]]  &&  maximum_parallel_io_streams=$max_par_io_str
779 [[ "$palmrun_tasks_per_node" != "" ]]  &&  tasks_per_node=$palmrun_tasks_per_node
780
781
782
783      # EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
784 if [[ $run_coupled_model = true ]] 
785 then
786
787    cores_atmos=`echo $coupled_dist | cut -d" " -s -f1`
788    cores_ocean=`echo $coupled_dist | cut -d" " -s -f2`
789
790    if (( $cores_ocean + $cores_atmos != $cores ))
791    then
792
793       printf "\n  +++ number of processors does not fit to specification by \"-Y\"."
794       printf "\n      PEs (total)     : $cores"
795       printf "\n      PEs (atmosphere): $cores_atmos"
796       printf "\n      PEs (ocean)     : $cores_ocean"
797       locat=coupling; exit
798
799    fi
800
801 fi
802
803
804    # IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES
805    # HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_...
806    # FOLDER
807 if [[ $running_in_batch_mode = true ]]
808 then
809 
810    if [[ ! -d ${fast_io_catalog}/${sources_for_run_catalog} ]]
811    then
812       printf "\n  +++ directory ${fast_io_catalog}/${sources_for_run_catalog} is missing"
813       printf "\n      Please check the output of the palmrun-call"
814       printf "\n      that you did on your local host."
815       locat=SOURCES_FOR_RUN; exit
816    fi
817
818 else
819
820       # CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN
821       # AUTOMATIC RESTART RUN
822       # AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
823    if [[ $restart_run = false ]]
824    then
825
826          # COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON
827          # THE LOCAL HOST
828       if [[ ! -d $source_path ]]
829       then
830          printf "\n\n  +++ source path \"$source_path\" on local host"
831          printf "\n      \"$(hostname)\" does not exist"
832          locat=source_path; exit
833       fi
834
835       rm -rf   ${base_directory}/${sources_for_run_catalog}
836       mkdir -p ${base_directory}/${sources_for_run_catalog}
837
838       if [[ "$source_list" = LM ]]
839       then
840
841             # DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
842          source_list=""
843          cd  $source_path
844
845
846             # CHECK, IF TRUNK-DIRECTORY IS UNDER SVN CONTROL
847          if [[ ! -d ../.svn ]]
848          then
849             printf "\n\n  +++ source directory"
850             printf "\n         \"$source_path\" "
851             printf "\n         is not under control of \"subversion\"."
852             printf "\n         Please do not use palmrun-option \"-s LM\"\n"
853          fi
854
855
856             # LIST ALL MODIFIED SOURCE CODE FILES
857          Filenames=""
858          svn status  >  tmp_svnstatus
859          while  read line
860          do
861             firstc=`echo $line | cut -c1`
862             if [[ $firstc = M  ||  $firstc = "?" ]]
863             then
864                Name=`echo "$line" | cut -c8-`
865                extension=`echo $Name | cut -d. -f2`
866                if [[ "$extension" = f90 || "$extension" = F90 || "$extension" = f || "$extension" = F || "$extension" = c ]]
867                then
868                   Filenames="$Filenames "$Name
869                fi
870             fi
871          done < tmp_svnstatus
872          rm -rf  tmp_svnstatus
873
874
875             # COPY FILES TO SOURCES_FOR_RUN_...
876          for  filename  in  $Filenames
877          do
878             cp  $filename  ${base_directory}/${sources_for_run_catalog}
879             source_list=$source_list"$filename "
880          done
881
882          cd -  > /dev/null
883
884
885          # COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
886       elif [[ "$source_list" != "" ]]
887       then
888
889          cd  $source_path
890
891          for  filename  in  $source_list
892          do
893
894                # SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
895             if [[ $(echo $filename | grep -c "/") != 0 ]]
896             then
897                printf "\n  +++ source code file:  $filename"
898                printf "\n      must not contain (\"/\") "
899                locat=source; exit
900             fi
901
902             if [[ ! -f $filename ]]
903             then
904                printf "\n  +++ source code file:  $filename"
905                printf "\n      does not exist"
906                locat=source; exit
907             else
908                cp  $filename  ${base_directory}/${sources_for_run_catalog}
909             fi
910
911          done
912
913          cd -  > /dev/null
914
915       fi
916
917          # CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
918       [[ "$makefile" = "" ]]  &&  makefile=$source_path/Makefile
919       if [[ ! -f $makefile ]]
920       then
921          printf "\n  +++ file \"$makefile\" does not exist"
922          locat=make; exit
923       else
924          cp  $makefile  ${base_directory}/${sources_for_run_catalog}/Makefile
925       fi
926
927
928          # COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
929       if [[ "$user_source_path" != "" ]]
930       then
931
932             # DOES THE DIRECTORY EXIST?
933          if [[ ! -d $user_source_path ]]
934          then
935
936             printf "\n\n  *** INFORMATIVE: additional source code directory"
937             printf "\n      \"$user_source_path\" "
938             printf "\n      does not exist or is not a directory."
939             printf "\n      No source code will be used from this directory!\n"
940             user_source_path=""
941             if [[ $silent == false ]]
942             then
943                sleep 2
944             fi
945
946          else
947
948             cd $user_source_path
949
950             Names=$(ls -1 *.f90 2>&1)
951             [[ $(echo $Names | grep -c '*.f90') = 0 ]]  &&  AddFilenames="$Names"
952             Names=$(ls -1 *.F90 2>&1)
953             [[ $(echo $Names | grep -c '*.F90') = 0 ]]  &&  AddFilenames="$AddFilenames $Names"
954             Names=$(ls -1 *.F 2>&1)
955             [[ $(echo $Names | grep -c '*.F') = 0   ]]  &&  AddFilenames="$AddFilenames $Names"
956             Names=$(ls -1 *.f 2>&1)
957             [[ $(echo $Names | grep -c '*.f') = 0   ]]  &&  AddFilenames="$AddFilenames $Names"
958             Names=$(ls -1 *.c 2>&1)
959             [[ $(echo $Names | grep -c '*.c') = 0   ]]  &&  AddFilenames="$AddFilenames $Names"
960
961             cd -  > /dev/null
962             cd  ${base_directory}/${sources_for_run_catalog}
963
964                # COPY MAKEFILE IF EXISTING
965             if [[ -f $user_source_path/Makefile ]]
966             then
967                printf "\n\n  *** user Makefile from directory"
968                printf "\n      \"$user_source_path\" is used \n"
969                if [[ $silent == false ]]
970                then
971                   sleep 1
972                fi
973                cp  $user_source_path/Makefile  .
974             fi
975
976             for  filename  in  $AddFilenames
977             do
978                if [[ -f $filename ]]
979                then
980                   printf "\n  +++ source code file \"$filename\" found in additional"
981                   printf "\n      source code directory \"$user_source_path\" "
982                   printf "\n      but was also given with option \"-s\" which means that it should be taken"
983                   printf "\n      from directory \"$source_path\"."
984                   locat=source; exit
985                fi
986
987                cp  $user_source_path/$filename  .
988                source_list="$source_list $filename"
989
990                   # CHECK IF FILE IS CONTAINED IN MAKEFILE
991                if [[ $(grep -c $filename Makefile) = 0 ]]
992                then
993                   printf "\n\n  +++ user file \"$filename\" "
994                   printf "\n      is not listed in Makefile \n"
995                   locat=source; exit
996                fi
997             done
998             cd -  > /dev/null
999          fi
1000       fi
1001
1002          # COPY CONFIGURATION FILES
1003       cp  $config_file  ${base_directory}/${sources_for_run_catalog}
1004       cp  $fileconnection_file  ${base_directory}/${sources_for_run_catalog}
1005
1006          # COPY SHELLSCRIPTS
1007       cp  ${source_path}/../SCRIPTS/palmrun    ${base_directory}/${sources_for_run_catalog}
1008       cp  ${source_path}/../SCRIPTS/batch_scp  ${base_directory}/${sources_for_run_catalog}
1009
1010    fi
1011
1012 fi
1013
1014
1015    # GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
1016    # (HANDED OVER TO RESTART-RUNS USING OPTION -G)
1017 if [[ "$global_revision" = "" ]]
1018 then
1019    global_revision=`svnversion $source_path  2>/dev/null`
1020    global_revision="Rev: $global_revision"
1021 fi
1022
1023
1024    # IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
1025 if [[ -n $cores ]]
1026 then
1027
1028       # CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
1029       # INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
1030    if [[ $tasks_per_node = 0 ]]
1031    then
1032       if [[ $create_batch_job = true  ||  $create_remote_batch_job = true ]]
1033       then
1034          printf "\n"
1035          printf "\n  +++ option \"-T\" (tasks per node) is missing"
1036          printf "\n      set -T option or define tasks_per_node in the config file"
1037          locat=tasks_per_node; (( iec = 0 )); exit
1038       else
1039             # DEFAULT FOR INTERACTIVE RUN
1040          tasks_per_node=$cores
1041       fi
1042    fi
1043
1044    if (( cores < tasks_per_node ))
1045    then
1046       printf "\n"
1047       printf "\n  +++ tasks per node (-T) cannot exceed total number of cores (-X)"
1048       printf "\n      given values: -T $tasks_per_node  -X $cores"
1049       locat=tasks_per_node; (( iec = 0 )); exit 
1050    fi
1051
1052    (( nodes = cores / ( tasks_per_node * threads_per_task ) ))
1053    (( mpi_tasks = cores / threads_per_task ))
1054    [[ $mpi_tasks = 0 ]]  &&  (( mpi_tasks = 1 ))
1055    (( ii = cores / tasks_per_node ))
1056    (( remaining_cores =  cores - ii * tasks_per_node ))
1057    if (( remaining_cores > 0 ))
1058    then
1059       printf "\n"
1060       printf "\n  +++ WARNING: tasks per node (option \"-T\") is not an integral"
1061       printf "\n      divisor of the total number of cores (option \"-X\")"
1062       printf "\n      values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\""
1063       printf "\n      One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks"
1064       (( nodes = nodes + 1 ))
1065    fi
1066
1067 fi
1068
1069
1070    # SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
1071 if [[ "$maximum_parallel_io_streams" = "" ]]
1072 then
1073    maximum_parallel_io_streams=$cores
1074 fi
1075
1076
1077    # SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT
1078 if [[ "$scp_port" != "" ]]
1079 then
1080    PORTOPT="-P $scp_port"
1081    SSH_PORTOPT="-p $scp_port"
1082 fi
1083
1084
1085    # DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
1086    # CONFIG-FILE
1087 if [[ "$ssh_key" != "" ]]
1088 then
1089    ssh_key="-i $HOME/.ssh/$ssh_key"
1090 fi
1091
1092
1093    # SET QUEUE, IF NOT GIVEN
1094 if [[ $create_batch_job = true  ||  $create_remote_batch_job = true ]]
1095 then
1096
1097    if [[ $queue = none  &&  "$defaultqueue" = "" ]]
1098    then
1099       printf "\n"
1100       printf "\n  +++ no default queue given in configuration file and no queue"
1101       printf "\n      given with option -q"
1102       locat=queue; exit
1103    fi
1104    if [[ $queue = none ]]
1105    then
1106       queue=$defaultqueue
1107    fi
1108
1109 fi
1110
1111
1112    # GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
1113    # CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
1114 (( i = 0 ))
1115 (( nr_of_input_files = 0 ))
1116 while (( i < iin ))
1117 do
1118    (( i = i + 1 ))
1119
1120       # GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1121       # FILE IDENTIFIER IS NOT PART OF THE FILENAME))
1122    if [[ "${actionin_pre[$i]}" = di ]]
1123    then
1124       eval filename=${pathin_pre[$i]}/${endin_pre[$i]}
1125    else
1126       eval filename=${pathin_pre[$i]}/${jobname}${endin_pre[$i]}
1127    fi
1128
1129
1130       # CHECK IF FILE EXISTS
1131    if ! ls $filename* 1>/dev/null 2>&1
1132    then
1133
1134          # FILES WITH ATTRIBUTE opt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
1135       if [[ "${optin_pre[$i]}" != "yes" ]]
1136       then
1137          printf "\n\n  +++ INPUT-file: "
1138          if [[ "${extin_pre[$i]}" = ""  ||  "${extin_pre[$i]}" = " " ]]
1139          then
1140             printf "\n           $filename"
1141          else
1142             printf "\n           $filename.${extin_pre[$i]}"
1143          fi
1144          printf "\n      does not exist\n"
1145          locat=input; exit
1146       else
1147          (( nr_of_input_files = nr_of_input_files + 1 ))
1148          localin[$nr_of_input_files]="${localin_pre[$i]}"
1149          optin[$nr_of_input_files]="${optin_pre[$i]}"
1150          actionin[$nr_of_input_files]="unavailable"
1151          pathin[$nr_of_input_files]="${pathin_pre[$i]}"
1152          endin[$nr_of_input_files]="${endin_pre[$i]}"
1153          extin[$nr_of_input_files]="${extin_pre[$i]}"
1154       fi
1155
1156    else
1157
1158          # FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME BASENAME ($jobname) AND
1159          # CREATE A LIST FOR THE DETECTED BASENAME ENDINGS
1160       if [[ "${multin[$i]}" = true ]]
1161       then
1162             # DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
1163          ls -1 -d ${filename}    >   filelist  2>/dev/null
1164          ls -1 -d ${filename}.*  >>  filelist  2>/dev/null
1165          ls -1 -d ${filename}_*  >>  filelist  2>/dev/null
1166
1167          endings=""
1168          while  read line
1169          do
1170                 # filename without path (i.e. after the last "/")
1171              basefilename=$(basename ${line})
1172
1173                 # check if there is an extension and remove it
1174              ext=${basefilename##*.}
1175              if [[ "$ext" = "${extin_pre[$i]}" ]]
1176              then
1177                 basefilename=${basefilename%.*}
1178              fi
1179
1180                 # check for an existing cycle number and remove it
1181              cycle=${basefilename##*.}
1182              if [[ $cycle =~ ^-?[0-9]+$ ]]
1183              then
1184                 basefilename=${basefilename%.*}
1185              fi
1186
1187                 # remove the jobname from the beginning
1188              length_jobname=${#jobname}
1189              ending=${basefilename:${length_jobname}}
1190
1191                 # remove the ending given in the .iofiles from the beginning
1192              endingstring="${endin_pre[$i]}"
1193              length_ending=${#endingstring}
1194              ending=${ending:${length_ending}}
1195
1196              if [[ "$ending" = "" ]]
1197              then
1198                    # standard ending as given in the .iofiles
1199                 if [[ $(echo $endings | grep -c DEFAULT) = 0 ]]
1200                 then
1201                    endings="$endings DEFAULT"
1202                 fi
1203              else
1204                    # ending must start with "_", otherwise its a different file
1205                 if [[ "${ending:0:1}" = "_" ]]
1206                 then
1207                    if [[ $(echo $endings | grep -c "$ending") = 0 ]]
1208                    then
1209                       endings="$endings $ending"
1210                    fi
1211                 fi
1212              fi
1213 
1214          done <filelist
1215
1216          rm filelist
1217
1218       else
1219
1220             # SINGLE NAME
1221          endings=DEFAULT
1222
1223       fi
1224
1225          # FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL INPUT FILE LIST
1226       for  ending  in  $endings
1227       do
1228
1229             # DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
1230          if [[ $ending = DEFAULT ]]
1231          then
1232             ending=""
1233          fi
1234
1235             # NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
1236          (( nr_of_input_files = nr_of_input_files + 1 ))
1237          localin[$nr_of_input_files]="${localin_pre[$i]}"$ending
1238          optin[$nr_of_input_files]="${optin_pre[$i]}"
1239          actionin[$nr_of_input_files]="${actionin_pre[$i]}"
1240          pathin[$nr_of_input_files]="${pathin_pre[$i]}"
1241          endin[$nr_of_input_files]="${endin_pre[$i]}"$ending
1242          extin[$nr_of_input_files]="${extin_pre[$i]}"
1243
1244
1245             # GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1246             # FILE IDENTIFIER IS NOT PART OF THE FILENAME))
1247          if [[ "${actionin[$nr_of_input_files]}" = di ]]
1248          then
1249             eval filename=${pathin[$nr_of_input_files]}/${endin[$nr_of_input_files]}
1250          else
1251             eval filename=${pathin[$nr_of_input_files]}/${jobname}${endin[$nr_of_input_files]}
1252          fi
1253
1254             # DETERMINE THE FILE'S CYCLE NUMBER
1255          (( maxcycle = 0 ))
1256          ls -1 -d $filename    >   filelist  2>/dev/null
1257          ls -1 -d $filename.*  >>  filelist  2>/dev/null
1258          while  read line
1259          do
1260                 # filename without path (i.e. after the last "/")
1261              basefilename=$(basename ${line})
1262   
1263                 # check if there is an extension
1264              extension=${basefilename##*.}
1265              if [[ "$extension" = "${extin[$nr_of_input_files]}" ]]
1266              then
1267                 basefilename=${basefilename%.*}
1268              fi
1269   
1270                 # check for an existing cycle number
1271              cycle=${basefilename##*.}
1272              if [[ $cycle =~ ^-?[0-9]+$ ]]
1273              then
1274                    # NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
1275                    # 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
1276                 (( icycle = $((10#$cycle)) ))
1277              else
1278                 (( icycle = 0 ))
1279              fi
1280   
1281              if (( icycle > maxcycle ))
1282              then
1283                 (( maxcycle = icycle ))
1284   
1285                    # FOR COMPATIBILITY REASONS WITH OLDER VERSIONS
1286                    # CHECK IF CYCLE NUMBER CONTAINS LEADING ZEROS
1287                 if [[ $(echo $cycle | cut -c1) = 0 ]]
1288                 then
1289                    leading_zero=true
1290                 else
1291                    leading_zero=false
1292                 fi
1293              fi
1294   
1295          done <filelist
1296          rm filelist
1297   
1298             # MAKE CYCLE NUMBER THREE DIGITS WIDE
1299          if [[ $leading_zero = true ]]
1300          then
1301             cyclestring=`printf "%03d" $maxcycle`
1302          else
1303             cyclestring=$maxcycle
1304          fi
1305   
1306             # APPEND CYCLE NUMBER TO FILENAME
1307          if (( maxcycle > 0 ))
1308          then
1309             if [[ "${extin[$nr_of_input_files]}" != " "  &&   "${extin[$nr_of_input_files]}" != "" ]]
1310             then
1311                filename=${filename}.$cyclestring.${extin[$nr_of_input_files]}
1312             else
1313                filename=${filename}.$cyclestring
1314             fi
1315          else
1316             if [[ "${extin[$nr_of_input_files]}" != " "  &&   "${extin[$nr_of_input_files]}" != "" ]]
1317             then
1318                filename=${filename}.${extin[$nr_of_input_files]}
1319             fi
1320          fi
1321         
1322             # STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1323             # IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
1324          absnamein[$nr_of_input_files]=$filename
1325          if (( maxcycle > 0 ))
1326          then
1327             if [[ "${actionin[$nr_of_input_files]}" = di ]]
1328             then
1329                frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}.$cyclestring
1330             else
1331                frelin[$nr_of_input_files]=${jobname}${endin[$nr_of_input_files]}.$cyclestring
1332             fi
1333          else
1334             if [[ "${actionin[$nr_of_input_files]}" = di ]]
1335             then
1336                frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}
1337             else
1338                frelin[$nr_of_input_files]=${jobname}${endin[$nr_of_input_files]}
1339             fi
1340          fi
1341
1342       done
1343
1344    fi
1345
1346 done
1347
1348
1349    # GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
1350    # CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
1351    # OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED 
1352    # THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRANSFERRED FROM THE REMOTE TO
1353    # THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
1354    # REMOTE HOST)
1355 (( i = 0 ))
1356 while (( i < iout ))
1357 do
1358    (( i = i + 1 ))
1359    if [[ ! ( $running_on_remote = true  &&  ( "${actionout_pre[$i]}" = tr || "${actionout_pre[$i]}" = tra || "${actionout_pre[$i]}" = trpe ) ) ]]
1360    then
1361       if [[ "${actionout_pre[$i]}" = tr ]]
1362       then
1363          actionout_pre[$i]=""
1364       elif [[ "${actionout_pre[$i]}" = trpe ]]
1365       then
1366          actionout_pre[$i]=pe
1367       elif [[ "${actionout_pre[$i]}" = tra ]]
1368       then
1369          actionout_pre[$i]=a
1370       fi
1371       (( maxcycle = 0 ))
1372       eval filename=${pathout_pre[$i]}/${jobname}${endout_pre[$i]}
1373       eval catalogname=${pathout_pre[$i]}
1374       if ! ls $filename* 1>/dev/null 2>&1
1375       then
1376     
1377             # IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
1378          if  cat /dev/null > $filename 
1379          then
1380             rm  $filename
1381          else
1382
1383                # CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
1384                # IF IT DOES NOT EXIST, TRY TO CREATE IT
1385             if [[ ! -d $catalogname ]]
1386             then
1387                if  mkdir -p  $catalogname
1388                then
1389                   printf "\n\n  *** directory:"
1390                   printf "\n           $catalogname"
1391                   printf "\n      was created\n"
1392                else
1393                   printf "\n\n  +++ OUTPUT-file:"
1394                   printf "\n           $filename"
1395                   printf "\n      cannot be created, because directory does not exist"
1396                   printf "\n      and cannot be created either"
1397                   printf "\n"
1398                   locat=output  ; exit
1399                fi 2>/dev/null
1400             else
1401                printf "\n\n  +++ OUTPUT-file:"
1402                printf "\n           $filename"
1403                printf "\n      cannot be created, although directory exists"
1404                printf "\n"
1405                locat=output  ; exit
1406             fi
1407          fi 2>/dev/null
1408
1409       fi
1410
1411    fi
1412 done
1413
1414
1415    # DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY
1416 if [[ $running_in_batch_mode = false ]]
1417 then
1418    run_id=$RANDOM
1419    job_id=${jobname}.$run_id
1420
1421    tempdir=$fast_io_catalog/$job_id
1422 fi
1423
1424
1425    # CHECK SETTINGS REQUIRED FOR BATCH JOBS
1426 if [[ $create_batch_job = true  ||  $create_remote_batch_job = true ]]
1427 then
1428
1429       # CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE
1430    if [[ $ibd = 0 ]]
1431    then
1432       printf "\n"
1433       printf "\n  +++ no batch directives found in configuration file"
1434       locat=config_file_batch_directives; (( iec = 0 )); exit 
1435    fi
1436
1437       # CHECK IF CPUTIME IS GIVEN FOR JOB
1438    done=false
1439    cputime=$cpumax
1440    while [[ $done = false ]]
1441    do
1442       if (( cputime == 0 ))
1443       then
1444          printf "\n  +++ cpu-time is undefined"
1445          printf "\n  >>> Please type CPU-time in seconds as INTEGER:"
1446          printf "\n  >>> "
1447          read  cputime   1>/dev/null  2>&1
1448       else
1449          done=true
1450       fi
1451    done
1452    cpumax=$cputime
1453
1454       # CHECK THE MEMORY DEMAND
1455    done=false
1456    while [[ $done = false ]]
1457    do
1458       if (( memory == 0 ))
1459       then
1460          printf "\n  +++ memory demand is undefined"
1461          printf "\n  >>> Please type memory in  MByte per process  as INTEGER:"
1462          printf "\n  >>> "
1463          read  memory  1>/dev/null  2>&1
1464       else
1465          done=true
1466       fi
1467    done
1468
1469       # IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
1470    if [[ $create_remote_batch_job = true  &&  -z $remote_username ]]
1471    then
1472       while [[ -z $remote_username ]]
1473       do
1474          printf "\n  +++ username on remote host with IP \"$remote_ip\" is undefined"
1475          printf "\n  >>> Please type username:"
1476          printf "\n  >>> "
1477          read  remote_username
1478       done
1479    fi
1480
1481 else
1482
1483    if [[ $running_in_batch_mode = false ]]
1484    then
1485       cputime=10000000  # NO LIMT FOR INTERACTIVE RUNS
1486       cpumax=$cputime
1487    else
1488       cputime=$cpumax
1489    fi
1490
1491 fi
1492
1493
1494    # CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES
1495 (( cpu_hours  = cputime / 3600 ))
1496 (( resttime = cputime - cpu_hours * 3600 ))
1497 (( cpu_minutes  = resttime / 60 ))
1498 (( cpu_seconds = resttime - cpu_minutes * 60 ))
1499 timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds}
1500
1501
1502    # OUTPUT OF THE PALMRUN-HEADER
1503 calltime=$(date)
1504 printf "\n"
1505 printf "#------------------------------------------------------------------------# \n"
1506 printf "| %-35s%35s | \n" "$version" "$calltime"
1507 printf "| %-35s%35s | \n" "PALM code    $global_revision" " "
1508 printf "|                                                                        | \n"
1509 column1="called on:"; column2=$(hostname)
1510 printf "| %-25s%-45s | \n" "$column1" "$column2"
1511 if [[ $create_remote_batch_job = true ]]
1512 then
1513    column1="execution on:"; column2="$host_configuration (username: $remote_username)"
1514 else
1515    if [[ $running_on_remote = true ]]
1516    then
1517       column1="host identifier:"; column2="$host_configuration (execute on IP: $remote_ip)"
1518    else
1519       column1="host identifier:"; column2="$host_configuration (execute on IP: $local_ip)"
1520    fi
1521 fi
1522 printf "| %-25s%-45s | \n" "$column1" "$column2"
1523
1524 column1="running in:"
1525 if [[ $running_in_batch_mode = true ]]
1526 then
1527    column2="batch job mode"
1528 else
1529    if [[ $create_batch_job = true  ||  $create_remote_batch_job = true ]]
1530    then
1531       column2="job creation mode"
1532    else
1533       column2="interactive run mode"
1534    fi
1535 fi
1536 printf "| %-25s%-45s | \n" "$column1" "$column2"
1537
1538 if  [[ $running_in_batch_mode = true  ||  $create_batch_job = true  ||  $create_remote_batch_job = true ]]
1539 then
1540    if [[ "$project_account" != "" ]]
1541    then
1542       column1="project account number:"
1543       column2="$project_account"
1544       printf "| %-25s%-45s | \n" "$column1" "$column2"
1545    fi
1546 fi
1547
1548 if [[ -n $cores ]]
1549 then
1550    if [[ $run_coupled_model = false ]]
1551    then
1552       column1="number of cores:"; column2=$cores
1553    else
1554       column1="number of cores:"; column2="$cores  (atmosphere: $cores_atmos, ocean: $cores_ocean)"
1555    fi
1556    printf "| %-25s%-45s | \n" "$column1" "$column2"
1557 fi
1558 if [[ -n $tasks_per_node ]]
1559 then
1560    column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)"
1561    printf "| %-25s%-45s | \n" "$column1" "$column2"
1562    if (( remaining_cores > 0 ))
1563    then
1564       column1=" "; column2="one of the nodes only filled with $remaining_cores tasks"
1565       printf "| %-25s%-45s | \n" "$column1" "$column2"
1566    fi
1567 fi
1568 if [[ $maximum_parallel_io_streams != $cores ]]
1569 then
1570    column1="max par io streams:"; column2="$maximum_parallel_io_streams"
1571    printf "| %-25s%-45s | \n" "$column1" "$column2"
1572 fi
1573 if [[ $use_openmp = true ]]
1574 then
1575    column1="threads per task:"; column2="$threads_per_task"
1576    printf "| %-25s%-45s | \n" "$column1" "$column2"
1577 fi
1578 if [[ $create_batch_job = true  ||  $create_remote_batch_job = true  ||  $running_in_batch_mode = true ]]
1579 then
1580    column1="memory demand / PE":; column2="$memory MB"
1581    printf "| %-25s%-45s | \n" "$column1" "$column2"
1582    column1="job cpu time (h:m:s):"; column2="$timestring"
1583    printf "| %-25s%-45s | \n" "$column1" "$column2"
1584 fi
1585 printf "|                                                                        | \n"
1586 if [[ "$source_list" != "" ]]
1587 then
1588    if [[ "$make_options" != "" ]]
1589    then
1590       column1="make options:"; column2=$(echo "$make_options" | cut -c-45)
1591       printf "| %-25s%-45s | \n" "$column1" "$column2"
1592       line=$(echo "$make_options" | cut -c46-)
1593       while [[ "$line" != "" ]]
1594       do
1595          column1=""
1596          column2=$(echo "$line" | cut -c-45)
1597          printf "| %-25s%-45s | \n" "$column1" "$column2"
1598          line=$(echo "$line" | cut -c46-)
1599       done
1600    fi
1601 fi
1602
1603 column1="cpp directives:"; column2=$(echo "$cpp_options" | cut -c-45)
1604 printf "| %-25s%-45s | \n" "$column1" "$column2"
1605 line=$(echo "$cpp_options" | cut -c46-)
1606 while [[ "$line" != "" ]]
1607 do
1608    column1=""
1609    column2=$(echo "$line" | cut -c-45)
1610    printf "| %-25s%-45s | \n" "$column1" "$column2"
1611    line=$(echo "$line" | cut -c46-)
1612 done
1613
1614 column1="compiler options:"; column2=$(echo "$compiler_options" | cut -c-45)
1615 printf "| %-25s%-45s | \n" "$column1" "$column2"
1616 line=$(echo "$compiler_options" | cut -c46-)
1617 while [[ "$line" != "" ]]
1618 do
1619    column1=""
1620    column2=$(echo "$line" | cut -c-45)
1621    printf "| %-25s%-45s | \n" "$column1" "$column2"
1622    line=$(echo "$line" | cut -c46-)
1623 done
1624
1625 column1="linker options:"; column2=$(echo "$linker_options" | cut -c-45)
1626 printf "| %-25s%-45s | \n" "$column1" "$column2"
1627 line=$(echo "$linker_options" | cut -c46-)
1628 while [[ "$line" != "" ]]
1629 do
1630    column1=""
1631    column2=$(echo "$line" | cut -c-45)
1632    printf "| %-25s%-45s | \n" "$column1" "$column2"
1633    line=$(echo "$line" | cut -c46-)
1634 done
1635
1636 if [[ "$login_init_cmd" != "" ]]
1637 then
1638    column1="login init commands:"; column2=$(echo "$login_init_cmd" | cut -c-45)
1639    printf "| %-25s%-45s | \n" "$column1" "$column2"
1640    line=$(echo "$login_init_cmd" | cut -c46-)
1641    while [[ "$line" != "" ]]
1642    do
1643       column1=""
1644       column2=$(echo "$line" | cut -c-45)
1645       printf "| %-25s%-45s | \n" "$column1" "$column2"
1646       line=$(echo "$line" | cut -c46-)
1647    done
1648 fi
1649
1650 if [[ "$module_commands" != "" ]]
1651 then
1652    column1="module commands:"; column2=$(echo "$module_commands" | cut -c-45)
1653    printf "| %-25s%-45s | \n" "$column1" "$column2"
1654    line=$(echo "$module_commands" | cut -c46-)
1655    while [[ "$line" != "" ]]
1656    do
1657       column1=""
1658       column2=$(echo "$line" | cut -c-45)
1659       printf "| %-25s%-45s | \n" "$column1" "$column2"
1660       line=$(echo "$line" | cut -c46-)
1661    done
1662 fi
1663 printf "|                                                                        | \n"
1664 column1="run identifier:"; column2=$jobname
1665 printf "| %-25s%-45s | \n" "$column1" "$column2"
1666 column1="activation string list:"; column2=$(echo $activation_string_list)
1667 printf "| %-25s%-45s | \n" "$column1" "$column2"
1668
1669 if [[ "$ocean_file_appendix" = true ]]
1670 then
1671    printf "| %-35s%-35s | \n" "suffix \"_O\" is added to local files" " "
1672 fi
1673
1674 if [[ "$source_list" != "" ]]
1675 then
1676    printf "|                                                                        | \n"
1677    printf "| Files to be compiled:                                                  | \n"
1678    line=$source_list
1679    while [[ "$line" != "" ]]
1680    do
1681       linestart=$(echo $line | cut -c-70)
1682       printf "| %-70s | \n" "$linestart"
1683       line=$(echo "$line" | cut -c71-)
1684    done
1685 fi
1686 printf "#------------------------------------------------------------------------#"
1687
1688
1689
1690    # OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
1691 if [[ $do_trace = true ]]
1692 then
1693    (( i = 0 ))
1694    while (( i < nr_of_input_files ))
1695    do
1696       (( i = i + 1 ))
1697       if (( i == 1 ))
1698       then
1699          printf "\n\n >>> INPUT-file assignments:\n"
1700       fi
1701       printf "\n     ${localin[$i]} :  ${absnamein[$i]}"
1702    done
1703    (( i = 0 ))
1704    while (( i < iout ))
1705    do
1706       (( i = i + 1 ))
1707       if (( i == 1 ))
1708       then
1709          printf "\n\n >>> OUTPUT-file assignments:\n"
1710       fi
1711       printf "\n     ${localout[$i]} :  ${pathout[$i]}"
1712    done
1713    (( i = 0 ))
1714    while (( i < iic ))
1715    do
1716       (( i = i + 1 ))
1717       if (( i == 1 ))
1718       then
1719          printf "\n\n >>> INPUT-commands:\n"
1720       fi
1721       printf "\n     ${in_command[$i]}" 
1722    done
1723    (( i = 0 ))
1724    while (( i < ioc ))
1725    do
1726       (( i = i + 1 ))
1727       if (( i == 1 ))
1728       then
1729          printf "\n\n >>> OUTPUT-commands:\n"
1730       fi
1731       printf "\n     ${out_command[$i]}" 
1732    done
1733 fi
1734
1735    # QUERY FOR CONTINUE
1736 if [[ $silent = false  &&  $running_in_batch_mode = false ]]
1737 then
1738    antwort=dummy
1739    printf "\n\n"
1740    printf " >>> everything o.k. (y/n) ?  "
1741    while  read antwort
1742    do
1743       if [[ "$antwort" != y  &&  "$antwort" != Y  &&  "$antwort" != n  &&  "$antwort" != N ]]
1744       then
1745          printf " >>> everything o.k. (y/n) ?  "
1746       else
1747          break
1748       fi
1749    done
1750    if [[ $antwort = n  ||  $antwort = N ]]
1751    then
1752       locat=user_abort; (( iec = 0 )); exit
1753    fi
1754    if [[ $create_batch_job = true  ||  $create_remote_batch_job = true ]]
1755    then
1756       printf "\n ***  batch-job will be created and submitted"
1757    else
1758       printf "\n ***  PALMRUN will now continue to execute on this machine"
1759    fi
1760 fi
1761
1762 
1763
1764    # PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE
1765 if [[ $restart_run = false  &&  $running_in_batch_mode = false ]]
1766 then
1767
1768    if [[ $create_batch_job = true  ||  $create_remote_batch_job  = true ]]
1769    then
1770       printf "\n\n  *** creating executable and other sources for the remote host\n"
1771    else
1772       printf "\n\n  *** creating executable and other sources for the local host\n"
1773    fi
1774
1775       # FIRST CHECK, IF A MAKE DEPOSITORY EXISTS, AND IF NOT, ASK THE USER IF
1776       # IT SHALL BE CREATED
1777    ask_for_make_depository=false
1778    if [[ $create_remote_batch_job = true ]]
1779    then
1780
1781       line=`grep %base_directory $config_file`
1782       make_depository=`echo $line | cut -d" " -s -f2`/MAKE_DEPOSITORY_${host_configuration}
1783       echo  "[[ ! -d ${make_depository} ]]  &&  echo depository not found" | ssh  -q  $ssh_key  ${remote_username}@${remote_ip} 2>&1  | tee ${host_configuration}_last_make_protokoll
1784
1785       if [[ $(grep -c "depository not found" ${host_configuration}_last_make_protokoll) != 0 ]]
1786       then
1787          printf "\n\n  +++ make depository \"${make_depository}\""
1788          printf "\n      on remote host not found!"
1789          ask_for_make_depository=true
1790       fi
1791       rm ${host_configuration}_last_make_protokoll
1792
1793    else
1794
1795          # CHECK FOR MAKE_DEPOSITORY ON THE LOCAL HOST
1796       make_depository=${base_directory}/MAKE_DEPOSITORY_${host_configuration}
1797       if [[ ! -d ${make_depository} ]]
1798       then
1799          printf "\n\n  +++ make depository \"${make_depository}\""
1800          printf "\n      on local host not found!"
1801          ask_for_make_depository=true
1802       fi
1803
1804    fi
1805
1806    if [[ $ask_for_make_depository = true ]]
1807    then
1808
1809       antwort=dummy
1810       printf "\n\n"
1811       printf "  >>> Create a new one (y/n) ?  "
1812       while  read antwort
1813       do
1814          if [[ "$antwort" != y  &&  "$antwort" != Y  &&  "$antwort" != n  &&  "$antwort" != N ]]
1815          then
1816             printf "  >>> Create a new one (y/n) ?  "
1817          else
1818             break
1819          fi
1820       done
1821       if [[ $antwort = n  ||  $antwort = N ]]
1822       then
1823          locat=user_abort; (( iec = 0 )); exit
1824       fi
1825
1826       if [[ $do_trace = true ]]
1827       then
1828          palmbuild  -h $host_configuration
1829       else
1830          palmbuild  -v  -h $host_configuration
1831       fi
1832
1833       if [[ $? != 0 ]]
1834       then
1835   
1836              # ABORT IN CASE OF COMPILATION PROBLEMS
1837          printf "\n  +++ error while compiling for the MAKE_DEPOSITORY"
1838          locat=make_depository
1839          exit
1840       else
1841          echo "  *** now continue with creating executable and other sources"
1842       fi
1843
1844    fi
1845
1846       # NOW CREATE THE SOURCES_FOR_RUN FOLDER
1847    palmbuild  -v  $use_existing_sources_folder  -h $host_configuration  -d $jobname
1848
1849    if [[ $? != 0 ]]
1850    then
1851
1852           # ABORT IN CASE OF COMPILATION PROBLEMS
1853       printf "\n  +++ error while creating executable and/or other sources"
1854       locat=execution
1855       rm -rf  ${base_directory}/${sources_for_run_catalog}
1856       exit
1857
1858    else
1859
1860       printf "  *** executable and other sources created\n"
1861       rm -rf  ${base_directory}/${sources_for_run_catalog}
1862
1863    fi
1864
1865 fi
1866
1867
1868    # WHEN CREATING A REMOTE BATCH JOB, THOSE INPUT FILES WITH TRANSFER-ATTRIBUT
1869    # WILL BE COPIED TO THE REMOTE HOST
1870 if [[ $create_remote_batch_job = true ]]
1871 then
1872    (( i = 0 ))
1873    while (( i < nr_of_input_files ))
1874    do
1875       (( i = i + 1 ))
1876       if [[ "${actionin[$i]}" = tr ]]
1877       then
1878          eval inputfile=${pathin[$i]}/${frelin[$i]}
1879          scp  -q $ssh_key  $PORTOPT  $inputfile  ${remote_username}@${remote_ip}:${fast_io_catalog}/${sources_for_run_catalog}/${frelin[$i]}
1880       fi
1881    done
1882    if (( i > 0 ))
1883    then
1884       printf "\n\n  *** input files have been copied to the remote host\n"
1885    fi
1886 fi
1887 
1888
1889    # NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
1890    # (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
1891 if [[ $create_batch_job = false  &&  $create_remote_batch_job = false ]]
1892 then
1893
1894       # CHANGE TO THE TEMPORARY WORKING DIRECTORY
1895    if [[ $running_in_batch_mode = false ]]
1896    then
1897          # CREATE THE DIRECTORY AND COPY FILES FROM SOURCES_FOR_RUN_... TO THAT
1898          # FOLDER
1899       mkdir -p  $tempdir
1900       chmod  go+rx  $tempdir
1901       cd  $tempdir
1902       cp  ${fast_io_catalog}/${sources_for_run_catalog}/{*,.[!.]*}  $tempdir
1903       printf "\n  *** changed to temporary directory: $tempdir"
1904
1905    else
1906
1907          # IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR
1908       printf "\n  *** running in temporary directory: $tempdir"
1909
1910    fi
1911
1912
1913       # PROVIDE THE INPUT FILES
1914       # LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
1915    optional_files_missing=false
1916    (( i = 0 ))
1917    while (( i < nr_of_input_files ))
1918    do
1919       (( i = i + 1 ))
1920       if (( i == 1 ))
1921       then
1922          printf "\n\n  *** providing INPUT-files:\n$dashes"
1923       fi
1924
1925
1926          # SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
1927       if [[ "${actionin[$i]}" = unavailable ]]
1928       then
1929          optional_files_missing=true
1930          continue
1931       fi
1932
1933          # CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
1934       files_for_cores=false; filetype=file
1935       if [[ "${actionin[$i]}" = pe  &&  -n $cores ]]
1936       then
1937          files_for_cores=true; filetype=files
1938          actionin[$i]=""
1939       elif [[ "${actionin[$i]}" = pe  &&  ! -n $cores ]]
1940       then
1941          actionin[$i]=""
1942       elif [[ "${actionin[$i]}" = lnpe  &&  -n $cores ]]
1943       then
1944          files_for_cores=true; filetype=files
1945          actionin[$i]="ln"
1946       elif [[ "${actionin[$i]}" = lnpe  &&  ! -n $cores ]]
1947       then
1948          actionin[$i]="ln"
1949       fi
1950
1951       if [[ $files_for_cores = true ]]
1952       then
1953          printf "\n  >>> INPUT: ${absnamein[$i]}/....  to  ${localin[$i]}"
1954       else
1955          printf "\n  >>> INPUT: ${absnamein[$i]}  to  ${localin[$i]}"
1956       fi
1957
1958          # INPUT-FILES TO BE LINKED
1959       if [[ "${actionin[$i]}" = ln ]]
1960       then
1961
1962          printf "\n      $filetype will be linked"
1963          if [[ $files_for_cores = false ]]
1964          then
1965             if [[ -f "${absnamein[$i]}" ]]
1966             then
1967                ln  ${absnamein[$i]}  ${localin[$i]}
1968                got_tmp[$i]=true
1969             fi
1970          else
1971             if [[ -d "${absnamein[$i]}" ]]
1972             then
1973                mkdir -p ${localin[$i]}
1974                cd ${absnamein[$i]}
1975                for file in $(ls *)
1976                do
1977                   ln $file $tempdir/${localin[$i]}
1978                done >|/dev/null 2>&1
1979                cd $tempdir
1980             fi
1981
1982                # IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
1983             if [[ ! -f "${localin[$i]}/_000000" ]]
1984             then
1985                printf "\n  --- WARNING: ln failed, using cp instead (might be time consuming...)"
1986                cp -r  ${absnamein[$i]}/*  ${localin[$i]}
1987             fi
1988
1989             got_tmp[$i]=true
1990          fi
1991       fi
1992
1993          # FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
1994       if [[ "${actionin[$i]}" = ""  ||  "${actionin[$i]}" = "di"  ||  "${actionin[$i]}" = "tr"  ||  "${actionin[$i]}" = "npe" ]]
1995       then
1996
1997          if [[ "${actionin[$i]}" = "npe"  &&  -n $cores ]]
1998          then
1999
2000                # FILE COPIES ARE PROVIDED FOR ALL CORES
2001                # EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
2002             printf "\n      file will be provided for $cores processors"
2003             mkdir -p ${localin[$i]}
2004             ival=$cores
2005             (( ii = 0 ))
2006             while (( ii <= ival-1 ))
2007             do
2008                if (( ii < 10 ))
2009                then
2010                   cp  ${absnamein[$i]}  ${localin[$i]}/_000$ii
2011                elif (( ii < 100 ))
2012                then
2013                   cp  ${absnamein[$i]}  ${localin[$i]}/_00$ii
2014                elif (( ii < 1000 ))
2015                then
2016                   cp  ${absnamein[$i]}  ${localin[$i]}/_0$ii
2017                else
2018                   cp  ${absnamein[$i]}  ${localin[$i]}/_$ii
2019                fi
2020                (( ii = ii + 1 ))
2021             done
2022
2023          else
2024
2025             if [[ $files_for_cores = true ]]
2026             then
2027
2028                   # PROVIDE FILES FOR EACH CORE
2029                   # FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
2030                   # FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
2031                printf "\n      providing $cores files for the respective cores"
2032                mkdir -p ${localin[$i]}
2033                        if [[ $link_local_input = true ]]
2034                              then
2035                                 printf "      files will be linked\n"
2036                                 cd ${absnamein[$i]}
2037                                 for file in $(ls *)
2038                                 do
2039                                    ln -f $file  ${localin[$i]}
2040                                 done
2041                                 cd $tempdir
2042                              fi
2043
2044                   # IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
2045                              if [[ ! -f "${localin[$i]}/_000000" ]]
2046                              then
2047                                 if [[ $link_local_input = true ]]
2048                                        then
2049                                        printf "\n  --- WARNING: ln failed, using cp instead (might be time consuming...)"
2050                                 fi
2051                                 cp -r  ${absnamein[$i]}/*  ${localin[$i]}
2052                              fi
2053
2054             else
2055
2056                   # PROVIDE FILE FOR RUNS ON A SINGLE CORE
2057                        if [[ $link_local_input = true ]]
2058                        then
2059                                 printf "      file will be linked\n"
2060                                 ln -f  ${absnamein[$i]}  ${localin[$i]}
2061                        fi
2062                                # If "ln -f" fails or if "$link_local_input = false" do a normal "cp"
2063                        if [[ ! -f "${localin[$i]}" ]]
2064                then
2065                                 if [[ $link_local_input = true ]]
2066                          then
2067                      printf "\n  --- WARNING: ln failed, using cp instead (might be time consuming...)"
2068                                 fi
2069                   if [[ $running_on_remote = true  &&  "${actionin[$i]}" = tr ]]
2070                   then
2071                      mv  ${absnamein[$i]}  ${localin[$i]}
2072                   else
2073                                 cp  ${absnamein[$i]}  ${localin[$i]}
2074                   fi
2075                fi
2076             fi
2077          fi
2078       fi
2079
2080    done
2081    if (( i != 0 ))
2082    then
2083       if [[ $optional_files_missing = true ]]
2084       then
2085          printf "\n  *** INFORMATIVE: some optional INPUT-files are not present"
2086       fi
2087       printf "\n$dashes\n  *** all INPUT-files provided \n"
2088    fi
2089
2090
2091       # EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
2092    (( i = 0 ))
2093    while (( i < iic ))
2094    do
2095       (( i = i + 1 ))
2096       if (( i == 1 ))
2097       then
2098          printf "\n\n  *** execution of INPUT-commands:\n$dashes"
2099       fi
2100       printf "\n  >>> ${in_command[$i]}"
2101       eval  ${in_command[$i]}
2102       if (( i == iic ))
2103       then
2104          printf "\n$dashes\n"
2105       fi
2106    done
2107
2108
2109       # CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
2110       # (FILE ENVPAR WILL BE READ BY PALM)
2111    cat  >  ENVPAR  <<  EOF
2112 &envpar  run_identifier = '$jobname', host = '$host_configuration',
2113          write_svf = .${write_svf}., write_binary = .${write_binary}.,
2114          read_svf = .${read_svf}., tasks_per_node = $tasks_per_node,
2115          maximum_parallel_io_streams = $maximum_parallel_io_streams,
2116          maximum_cpu_time_allowed = ${cpumax}.,
2117          revision = '$global_revision',
2118          batch_job = .${running_in_batch_mode}. /
2119
2120EOF
2121
2122
2123       # STARTING THE EXECUTABLE
2124    printf "\n\n  *** execution starts in directory\n      \"`pwd`\"\n$dashes\n"
2125    PATH=$PATH:$tempdir
2126
2127
2128       # REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES
2129    line=`echo  "${execute_command}" | sed 's/{{/$/g' | sed 's/}}//g'`
2130    line2=`echo  "${execute_command}" | sed 's/{{mpi_tasks}}/1/g' | sed 's/{{tasks_per_node}}/1/g' | sed 's/palm/combine_plot_fields.x/g'`
2131    eval line=\"$line\"
2132    execute_command="$line"
2133
2134
2135       # EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS
2136    if [[ "$execute_command_for_combine" = "" ]]
2137    then
2138       eval line2=\"$line2\"
2139       execute_command_for_combine="$line2"
2140    fi
2141   
2142
2143
2144       # PROVIDE A HOSTFILE, IF REQUIRED
2145    if [[ "$hostfile" != "" ]]
2146    then
2147
2148       if [[ $hostfile = auto ]]
2149       then
2150             # CREATE A NEW HOSTFILE
2151          (( ii = 1 ))
2152          while (( ii <= cores / threads_per_task ))
2153          do
2154             echo  $(hostname)  >>  hostfile
2155             (( ii = ii + 1 ))
2156          done
2157          if (( cores / threads_per_task == 0 ))
2158          then
2159             echo  $(hostname)  >>  hostfile
2160          fi
2161       
2162       else
2163          cp  $hostfile  hostfile
2164       fi
2165       eval line=\"`head -n $ii  hostfile`\"
2166       printf "\n  *** running on: $line"
2167    fi
2168
2169
2170
2171       # SET THE NUMBER OF OPENMP-THREADS
2172    if [[ $use_openmp = true ]]
2173    then
2174       export OMP_NUM_THREADS=$threads_per_task
2175       printf "\n  *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS"
2176    else
2177       export OMP_NUM_THREADS=1
2178    fi
2179
2180
2181       # PROVIDE DATA FOR ATMOSPHERE OCEAN COUPLING
2182    if [[ $run_coupled_model = false ]]
2183    then
2184       if [[ "$ocean_file_appendix" = true ]]
2185       then
2186          echo "precursor_ocean"  >  coupling_steering
2187       else
2188          echo "precursor_atmos"  >  coupling_steering
2189      fi
2190    else
2191       (( iia = $cores_atmos / $threads_per_task ))
2192       (( iio = $cores_ocean / $threads_per_task ))
2193       printf "\n      coupled run ($iia atmosphere, $iio ocean)"
2194       printf "\n\n"
2195       echo "coupled_run $iia $iio"  >  coupling_steering
2196    fi
2197
2198    printf "\n  *** execute command:"
2199    printf "\n      \"$execute_command\" \n\n"
2200
2201    $execute_command  <  coupling_steering
2202
2203    if [[ $? != 0 ]]
2204    then
2205
2206           # ABORT IN CASE OF RUNTIME ERRORS
2207       printf "\n  +++ runtime error occured"
2208       locat=execution
2209       exit
2210
2211    else
2212
2213       printf "\n$dashes\n  *** execution finished \n"
2214
2215    fi
2216
2217
2218       # CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
2219       # BY EACH CORE INTO ONE FILE
2220   if [[ ! -f combine_plot_fields.x ]]
2221   then
2222
2223      printf "\n\n\n  +++ WARNING: no combine_plot_fields found"
2224      printf "\n      2d- and/or 3d-data may be incomplete!"
2225      printf "\n      Your previous palmbuild may have failed. Please check.\n"
2226
2227   elif [[ "$combine_plot_fields" == true ]]
2228   then
2229
2230      printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..."
2231      $execute_command_for_combine
2232
2233   else
2234
2235         # TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
2236         # DATA OUTPUT
2237      printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
2238   fi
2239
2240
2241
2242       # EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
2243    (( i = 0 ))
2244    while (( i < ioc ))
2245    do
2246       (( i = i + 1 ))
2247       if (( i == 1 ))
2248       then
2249          printf "\n\n  *** execution of OUTPUT-commands:\n$dashes"
2250       fi
2251
2252          # REPLACE PARAMETERS IN THE OUTPUT COMMAND WITH REAL VALUES
2253       out_command[$i]=`echo  "${out_command[$i]}" | sed 's/{{/$/g' | sed 's/}}//g'`
2254
2255       printf "\n  >>> ${out_command[$i]}"
2256       eval  ${out_command[$i]}
2257       if (( i == ioc ))
2258       then
2259          printf "\n$dashes\n"
2260       fi
2261    done
2262
2263
2264       # IN A FIRST PASS, ADD ADDITIONAL OUTPUT FILE CONNECTIONS IN CASE OF
2265       # WILDCARDS
2266    (( i = 0 ))
2267    (( nr_of_output_files = 0 ))
2268
2269    while (( i < iout ))
2270    do
2271
2272       (( i = i + 1 ))
2273
2274          # FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME LOCAL NAME AND
2275          # CREATE A LIST FOR THE DETECTED ENDINGS
2276       if [[ "${multout[$i]}" = true ]]
2277       then
2278             # DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
2279          ls -1 -d ${localout_pre[$i]}    >   filelist  2>/dev/null
2280          ls -1 -d ${localout_pre[$i]}_*  >>  filelist  2>/dev/null
2281
2282          endings="DEFAULT"
2283          while  read line
2284          do
2285                 # remove the local name from the beginning
2286              localnamestring="${localout_pre[$i]}"
2287              length_localname=${#localnamestring}
2288              ending=${line:${length_localname}}
2289
2290              if [[ "$ending" != "" ]]
2291              then
2292                 endings="$endings $ending"
2293              fi
2294 
2295          done <filelist
2296
2297          rm filelist
2298
2299       else
2300
2301             # SINGLE NAME
2302          endings=DEFAULT
2303
2304       fi
2305
2306          # FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL OUTPUT FILE LIST
2307       for  ending  in  $endings
2308       do
2309
2310             # DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
2311          if [[ $ending = DEFAULT ]]
2312          then
2313             ending=""
2314          fi
2315
2316             # NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
2317          (( nr_of_output_files = nr_of_output_files + 1 ))
2318          localout[$nr_of_output_files]="${localout_pre[$i]}"$ending
2319          transout[$nr_of_output_files]="${transout_pre[$i]}"
2320          actionout[$nr_of_output_files]="${actionout_pre[$i]}"
2321          pathout[$nr_of_output_files]="${pathout_pre[$i]}"
2322          endout[$nr_of_output_files]="${endout_pre[$i]}"$ending
2323          extout[$nr_of_output_files]="${extout_pre[$i]}"
2324          warnout[$nr_of_output_files]="${warnout_pre[$i]}"
2325
2326       done
2327
2328    done
2329
2330
2331
2332
2333       # COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
2334    (( i = 0 ))
2335    while (( i < nr_of_output_files ))
2336    do
2337       (( i = i + 1 ))
2338       if (( i == 1 ))
2339       then
2340          printf "\n\n  *** saving OUTPUT-files:"
2341
2342             # GET RUN NUMBER ASSIGNED BY PALM
2343          if [[ -f RUN_NUMBER ]]
2344          then
2345              read  run_number  <  RUN_NUMBER
2346              printf "\n  *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
2347              usecycle_option="-U $run_number"
2348          else
2349              run_number=0
2350              usecycle_option=""
2351          fi
2352          if [[ $running_on_remote = true  &&  "$remote_loginnode" != "" ]]
2353          then
2354             printf "\n  *** in case of SCP transfers to local host"
2355             printf "\n      they will be done via remote login-node \"$remote_loginnode\" "
2356          fi
2357          printf "\n$dashes"
2358       fi
2359
2360       if [[ ! ( $running_on_remote = true  &&  ( "${actionout[$i]}" = tr || "${actionout[$i]}" = tra || "${actionout[$i]}" = trpe ) ) ]]
2361       then
2362
2363          eval filename=${pathout[$i]}/${jobname}${endout[$i]}
2364
2365             # DETERMINE THE CYCLE NUMBER
2366          ls -1 -d $filename    >   filelist  2>/dev/null
2367          ls -1 -d $filename.*  >>  filelist  2>/dev/null
2368          while  read line
2369          do
2370   
2371                # filename without path (i.e. after the last "/")
2372             basefilename=$(basename ${line})
2373   
2374                # check if there is an extension
2375             extension=${basefilename##*.}
2376             if [[ "$extension" = "${extout[$i]}" ]]
2377             then
2378                basefilename=${basefilename%.*}
2379             fi
2380   
2381                # check for an existing cycle number
2382             cycle=${basefilename##*.}
2383             if [[ $cycle =~ ^-?[0-9]+$ ]]
2384             then
2385                   # NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
2386                   # 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
2387                (( icycle = $((10#$cycle)) + 1 ))
2388             else
2389                (( icycle = 1 ))
2390             fi
2391   
2392             if (( icycle > maxcycle ))
2393             then
2394                (( maxcycle = icycle ))
2395             fi
2396   
2397          done <filelist
2398          rm filelist
2399
2400   
2401             # SET THE CYCLE NUMBER
2402             # IN CASE OF FILE-APPEND, IT MUST BE THE HIGHEST EXISTING CYCLE NUMBER
2403          if [[ "${actionout[$i]}" = a ]]
2404          then
2405             (( maxcycle = maxcycle - 1 ))
2406          fi
2407         
2408          (( cycnum[$i] = maxcycle ))
2409          pathout[$i]=$filename
2410
2411
2412             # ADD CYCLE NUMBER TO FILENAME
2413             # IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
2414          if [[ "${actionout[$i]}" != "a" ]]
2415          then
2416                # SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
2417                # WITH AN EXISTING CYCLE NUMBER
2418             if (( run_number >= cycnum[$i] ))
2419             then
2420                (( cycnum[$i] = run_number ))
2421             else
2422                if (( run_number > 0 ))
2423                then
2424                   printf "\n  --- INFORMATIVE: The following file cannot get a unified cycle number"
2425                fi
2426             fi
2427          fi
2428          if (( cycnum[$i] > 0 ))
2429          then
2430             cyclestring=`printf "%03d" ${cycnum[$i]}`
2431             pathout[$i]=${pathout[$i]}.$cyclestring
2432          fi
2433       fi           
2434
2435          # CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
2436       files_for_cores=false; filetype=file
2437       link_local_output=false
2438       if [[ "${actionout[$i]}" = pe  &&  -n $cores ]]
2439       then
2440          files_for_cores=true; filetype=directory
2441          actionout[$i]=""
2442       elif [[ "${actionout[$i]}" = pe  &&  ! -n $cores ]]
2443       then
2444          actionout[$i]=""
2445       elif [[ "${actionout[$i]}" = lnpe  &&  -n $cores ]]
2446       then
2447          files_for_cores=true; filetype=directory
2448          link_local_output=true
2449          actionout[$i]=""
2450       elif [[ "${actionout[$i]}" = lnpe  &&  ! -n $cores ]]
2451       then
2452          link_local_output
2453          actionout[$i]=""
2454       elif [[ "${actionout[$i]}" = trpe  &&  -n $cores ]]
2455       then
2456          files_for_cores=true; filetype=directory
2457          actionout[$i]="tr"
2458       elif [[ "${actionout[$i]}" = trpe  &&  ! -n $cores ]]
2459       then
2460          actionout[$i]="tr"
2461       fi
2462
2463       if [[ ! -f ${localout[$i]}  &&  $files_for_cores = false ]]
2464       then
2465          if [[ ${warnout[$i]} = true ]]
2466          then
2467             printf "\n  +++ temporary OUTPUT-file  ${localout[$i]}  does not exist\n"
2468          fi
2469       elif [[ ! -d ${localout[$i]}  &&  $files_for_cores = true ]]
2470       then
2471          if [[ ${warnout[$i]} = true ]]
2472          then
2473             printf "\n  +++ temporary OUTPUT-file  ${localout[$i]}/....  does not exist\n"
2474          fi
2475       else
2476
2477
2478             # COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
2479             # IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
2480          if [[ "${actionout[$i]}" = tr  ||  "${actionout[$i]}" = tra ]]
2481          then
2482             if [[ $running_on_remote = true ]]
2483             then
2484
2485                   # SET OPTIONS FOR TRANSFER
2486                if [[ "${actionout[$i]}" = tr ]]
2487                then
2488                   if [[ $files_for_cores = false ]]
2489                   then
2490                      catalog_option=""
2491                      catalog_string=""
2492                   else
2493                      catalog_option="-c"
2494                      catalog_string="/"
2495                   fi
2496                   append_option=""
2497                   append_string=""
2498                else
2499                   append_option="-A"
2500                   append_string="append"
2501                fi
2502
2503                transfer_failed=false
2504                printf "\n  >>> OUTPUT: ${localout[$i]}$catalog_string  $append_string by SCP to"
2505                printf "\n              ${pathout[$i]}/${host_configuration}_${jobname}${endout[$i]}$catalog_string\n"
2506
2507                   # TRANSFER VIA SCP
2508                if [[ "$remote_loginnode" != "" ]]
2509                then
2510                   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]}\" ${host_configuration}_${jobname}${endout[$i]}  ${extout[$i]}"  |  ssh -q $remote_username@$remote_loginnode
2511                else
2512                   batch_scp $PORTOPT $catalog_option $append_option -b -m $usecycle_option -u $local_username $return_address  ${localout[$i]} "${pathout[$i]}" ${host_configuration}_${jobname}${endout[$i]}  ${extout[$i]}
2513                fi
2514                [[ $? != 0 ]]  &&  transfer_failed=true
2515
2516
2517                   # IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
2518                if [[ $transfer_failed = true ]]
2519                then
2520                   printf "  +++ transfer failed. Trying to save a copy on this host under:\n"
2521                   printf "      ${pathout[$i]}/${host_configuration}_${jobname}${endout[$i]}_$run_id\n"
2522
2523                      # FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
2524                   eval  local_catalog=${pathout[$i]}
2525                   if [[ ! -d $local_catalog ]]
2526                   then
2527                      printf "  *** local directory does not exist. Trying to create:\n"
2528                      printf "      $local_catalog \n"
2529                      mkdir -p  $local_catalog
2530                   fi
2531                   eval  cp  ${localout[$i]}  ${pathout[$i]}/${host_configuration}_${jobname}${endout[$i]}_$run_id
2532                   transfer_problems=true
2533                fi
2534
2535             else
2536
2537                   # UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST
2538                   # BE COPIED OR APPENDED ON THIS MACHINE
2539                if [[ "${actionout[$i]}" = tr ]]
2540                then
2541                   actionout[$i]=""
2542                else
2543                   actionout[$i]="a"
2544                fi
2545             fi
2546          fi
2547
2548
2549             # APPEND ON THIS MACHINE
2550          if [[ "${actionout[$i]}" = "a" ]]
2551          then
2552             if [[ "${extout[$i]}" != " "  &&  "${extout[$i]}" != "" ]]
2553             then
2554                printf "\n  >>> OUTPUT: ${localout[$i]}  append to"
2555                printf "\n              ${pathout[$i]}.${extout[$i]}\n"
2556                cat  ${localout[$i]}  >>  ${pathout[$i]}.${extout[$i]}
2557             else
2558                printf "\n  >>> OUTPUT: ${localout[$i]}  append to"
2559                printf "\n              ${pathout[$i]}\n"
2560                cat  ${localout[$i]}  >>  ${pathout[$i]}
2561             fi
2562          fi
2563
2564             # COPY ON THIS MACHINE
2565             # COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
2566             # ON DIFFERENT FILE-SYSTEMS
2567          if [[ "${actionout[$i]}" = ""  &&  $files_for_cores = false ]]
2568          then
2569
2570                # COPY IN CASE OF RUNS ON SINGLE CORES
2571             if [[ "${extout[$i]}" != " "  &&  "${extout[$i]}" != "" ]]
2572             then
2573                printf "\n  >>> OUTPUT: ${localout[$i]}  to"
2574                printf "\n              ${pathout[$i]}.${extout[$i]}\n"
2575                              if [[ $link_local_output = true ]]
2576                              then
2577                                 printf "      file will be linked\n"
2578                                 ln -f  ${localout[$i]}  ${pathout[$i]}.${extout[$i]}
2579                              fi
2580                                 # If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
2581                              if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
2582                then
2583                                 if [[ $link_local_output = true ]]
2584                          then
2585                      printf "  --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2586                                 fi
2587                                 cp  ${localout[$i]}  ${pathout[$i]}.${extout[$i]}
2588                              else
2589                   printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
2590                fi
2591             else
2592                printf "\n  >>> OUTPUT: ${localout[$i]}  to"
2593                printf "\n              ${pathout[$i]}\n"
2594                              if [[ $link_local_output = true ]]
2595                              then
2596                                 printf "      file will be linked\n"
2597                                 ln -f  ${localout[$i]}  ${pathout[$i]}
2598                              fi
2599                                 # If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
2600                        if [[ ! -f "${pathout[$i]}" ]]
2601                then
2602                                 if [[ $link_local_output = true ]]
2603                          then
2604                      printf "  --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2605                                 fi
2606                                 cp  ${localout[$i]}  ${pathout[$i]}
2607                              else
2608                                 printf "+++ no copy because file ${pathout[$i]} exists\n"
2609                fi
2610             fi
2611
2612          elif [[ "${actionout[$i]}" = ""  &&  $files_for_cores = true ]]
2613          then
2614
2615                # FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
2616                # AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
2617             printf "\n  >>> OUTPUT: ${localout[$i]}/_....  to"
2618             printf "\n              ${pathout[$i]}\n"
2619                    if [[ $link_local_output = true ]]
2620                    then
2621                              printf "      files will be linked\n"
2622                              mkdir -p ${pathout[$i]}
2623                              cd ${localout[$i]}
2624                              for file in $(ls *)
2625                              do
2626                                 ln -f $file  ${pathout[$i]}
2627                              done >|/dev/null 2>&1
2628                              cd $tempdir
2629                    fi
2630
2631                # IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
2632                    if [[ ! -f "${pathout[$i]}/_000000" ]]
2633             then
2634                              if [[ $link_local_output = true ]]
2635                              then
2636                   printf "  --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2637                              fi
2638                              [[ ! -d "${pathout[$i]}" ]]  &&  mkdir  ${pathout[$i]}
2639                              cp -r  ${localout[$i]}/*  ${pathout[$i]}
2640             fi
2641
2642          fi
2643       fi
2644    done
2645
2646    if (( i != 0 ))
2647    then
2648       if [[ $transfer_problems = true ]]
2649       then
2650          printf "\n$dashes\n  *** OUTPUT-files saved"
2651          printf "\n  +++ WARNING: some data transfers failed! \n"
2652       else
2653          printf "\n$dashes\n  *** all OUTPUT-files saved \n"
2654       fi
2655    fi
2656
2657
2658       # IF REQUIRED, START A RESTART-JOB
2659       # FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
2660    if [[ -f CONTINUE_RUN ]]
2661    then
2662
2663          # ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY):
2664          # -C TELLS PALMRUN THAT IT IS A RESTART-RUN
2665          # -v SILENT MODE WITHOUT INTERACTIVE QUERIES
2666          # -b START A BATCH JOB
2667       [[ $(echo $prc | grep -c "\-C") = 0 ]]  &&  prc="$prc -C"
2668       [[ $(echo $prc | grep -c "\-v") = 0 ]]  &&  prc="$prc -v"
2669       [[ $(echo $prc | grep -c "\-b") = 0 ]]  &&  prc="$prc -b"
2670
2671          # REPLACE SVFOUT IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
2672          # SO THAT RESTARTS USE SVF DATA CREATED BY THE INITIAL RUN
2673       if [[ $(echo $prc | grep -c "svfout") != 0 ]]
2674       then
2675          prc=`echo $prc | sed 's/svfout/svfin/g'`
2676       fi
2677
2678          # REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
2679          # SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN
2680       if [[ $(echo $prc | grep -c "#") != 0 ]]
2681       then
2682          prc=`echo $prc | sed 's/#/r/g'`
2683       fi
2684
2685
2686          # START THE RESTART-JOB
2687       printf "\n\n  *** initiating restart-run on \"$local_ip\" using command:\n"
2688       echo "      $prc"
2689       printf "\n$dashes\n"
2690       if [[ $running_on_remote = true ]]
2691       then
2692
2693          echo "*** ssh will be used to initiate restart-runs!"
2694          echo "    return_address=\"$return_address\" "
2695          echo "    return_username=\"$local_username\" "
2696
2697          if [[ "$remote_loginnode" != "" ]]
2698          then
2699             echo "echo \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" |  ssh -q $SSH_PORTOPT  $local_username@$return_address  " |  ssh -q $remote_username@$remote_loginnode  |  tee palmrun_restart.log
2700          else
2701             echo \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" |  ssh -q $SSH_PORTOPT  $local_username@$return_address  |  tee palmrun_restart.log
2702          fi
2703
2704             # WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
2705          sleep 30
2706
2707       else
2708
2709             # START THE RESTART JOB ON THE LOCAL HOST
2710          eval  $prc  |  tee palmrun_restart.log              # THE ' MUST BE EVALUATED
2711          cd -  > /dev/null
2712
2713       fi
2714
2715          # CHECK, IF RESTART JOB HAS BEEN STARTED
2716       if [[ $( grep -c "+++ palmrun killed"  palmrun_restart.log ) != 0 ]]
2717       then
2718          printf "\n$dashes\n  +++ creating restart run failed \n"
2719          locat=create_restart
2720          exit
2721          rm  palmrun_restart.log
2722       else
2723          printf "\n$dashes\n  *** restart run initiated \n"
2724          rm  palmrun_restart.log
2725       fi
2726
2727
2728          # DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
2729          # DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
2730          # THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
2731          # MAY BE VERY HUGE)
2732       (( i = 0 ))
2733       while (( i < nr_of_input_files ))
2734       do
2735          (( i = i + 1 ))
2736          if [[ "${got_tmp[$i]}" = true   &&  $keep_data_from_previous_run = false ]]
2737          then
2738             rm -r  ${absnamein[$i]}
2739          fi
2740       done
2741
2742    fi
2743
2744
2745       # ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
2746    cd  $HOME
2747    [[ $delete_temporary_catalog = true ]]  &&  rm -rf $tempdir
2748
2749
2750 else
2751
2752
2753       # PREPARING ACTIONS,
2754       # IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE
2755
2756       # BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB
2757    palmrun_com="$palmrun_script_name -d $jobname -h $host_configuration -m $memory -t $cpumax -q $queue -r $run_id -U $local_username"
2758    [[ "$activation_string_list" != "" ]]  &&  palmrun_com=${palmrun_com}" -a \"$activation_string_list\""
2759    [[ "$global_revision" != "" ]]  &&  palmrun_com=${palmrun_com}" -G \"$global_revision\""
2760    [[ $keep_data_from_previous_run = true ]]  &&  palmrun_com=${palmrun_com}" -k"
2761    [[ $do_trace = true ]]        &&  palmrun_com=${palmrun_com}" -x"
2762    [[ "$cores" != "" ]]       &&  palmrun_com=${palmrun_com}" -X $cores"
2763    [[ $use_openmp = true ]]  &&  palmrun_com=${palmrun_com}" -O $threads_per_task"
2764    [[ $tasks_per_node != 0 ]]  &&  palmrun_com=${palmrun_com}" -T $tasks_per_node"
2765    [[ $delete_temporary_catalog = false ]]  &&  palmrun_com=${palmrun_com}" -B"
2766    [[ "$ocean_file_appendix" = true ]]  &&  palmrun_com=${palmrun_com}" -y"
2767    [[ $run_coupled_model = true ]]  &&  palmrun_com=${palmrun_com}" -Y \"$coupled_dist\""
2768    [[ "$combine_plot_fields" = false ]]  &&  palmrun_com=${palmrun_com}" -Z"
2769    [[ "$max_par_io_str" != "" ]]  &&  palmrun_com=${palmrun_com}" -w $max_par_io_str"
2770    [[ "$project_account" != "" ]]  &&  palmrun_com=${palmrun_com}" -A $project_account"
2771    if [[ $create_remote_batch_job = true ]]
2772    then
2773       palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip"
2774       if [[ $do_trace = true ]]
2775       then
2776          printf "\n *** PALMRUN-command on remote host:\n     $palmrun_com \n"
2777       fi
2778    elif [[ $create_batch_job = true ]]
2779    then
2780       palmrun_com=${palmrun_com}" -j"
2781       if [[ $do_trace = true ]]
2782       then
2783          printf "\n *** PALMRUN-command on local host:\n     $palmrun_com \n"
2784       fi
2785    fi
2786
2787
2788       # DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND
2789       # REMOTE HOST
2790    job_protocol_file_local=${local_jobcatalog}/${host_configuration}_${job_id}
2791    job_protocol_file=$job_protocol_file_local
2792    if [[ $create_remote_batch_job = true ]]
2793    then
2794       job_protocol_file_remote=${remote_jobcatalog}/${host_configuration}_${job_id}
2795       job_protocol_file=$job_protocol_file_remote
2796       job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol
2797       scpjob_file=${remote_jobcatalog}/scpjob.$run_id
2798    fi
2799
2800
2801       # BUILD THE JOB-SCRIPTS ON FILE jobfile
2802    jobfile=jobfile.$run_id
2803
2804
2805       # FIRST CREATE THE BATCH DIRECTIVES
2806    (( i = 0 ))
2807    while (( i < ibd ))
2808    do
2809       (( i = i + 1 ))
2810       line=`echo  "${batch_directive[$i]}" | sed 's/{{/$/g' | sed 's/}}//g'`
2811       eval line=\"$line\"
2812       echo  "$line"                               >>  $jobfile
2813    done
2814    echo " "                                       >>  $jobfile
2815
2816
2817       # FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB
2818       # PROTOCOL
2819    if [[ $create_remote_batch_job = true ]]
2820    then
2821       echo "set +vx"                              >>  $jobfile
2822       echo "trap '"                               >>  $jobfile
2823       echo "set +vx"                              >>  $jobfile
2824       echo "cd ${remote_jobcatalog}"              >>  $jobfile
2825       echo "cat >  scpjob.$run_id << %%END%%"     >>  $jobfile
2826
2827          # ADD THE BATCH DIRECTIVES
2828       (( i = 0 ))
2829       while (( i < ibdt ))
2830       do
2831          (( i = i + 1 ))
2832          line=`echo  "${batch_directive_transfer[$i]}" | sed 's/{{/$/g' | sed 's/}}//g'`
2833          eval line=\"$line\"
2834          echo  "$line"                            >>  $jobfile
2835       done
2836       echo " "                                    >>  $jobfile
2837
2838       echo "set -x"                               >>  $jobfile
2839       echo "${fast_io_catalog}/${sources_for_run_catalog}/batch_scp  $PORTOPT  -d  -w 10  -u $local_username $local_ip  $job_protocol_file_remote  \"$local_jobcatalog\"  ${host_configuration}_${jobname}"  >>  $jobfile
2840       echo "%%END%%"                              >>  $jobfile
2841       echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" "  >>  $jobfile
2842       echo "$submit_command  $scpjob_file"        >>  $jobfile
2843       echo "rm $scpjob_file"                      >>  $jobfile
2844       echo "rm -rf $job_transfer_protocol_file"   >>  $jobfile
2845       echo "set -x"                               >>  $jobfile
2846       echo "     ' exit"                          >>  $jobfile
2847    fi
2848
2849
2850       # ACTIVATE ERROR-TRACEBACK
2851    if [[ $do_trace = true ]]
2852    then
2853       echo  "set -x"                                    >>  $jobfile
2854    else
2855       echo  "set +vx"                                   >>  $jobfile
2856    fi
2857
2858
2859       # INITIALIZE THE ENVIRONMENT AND LOAD MODULES
2860    if [[ "$login_init_cmd" != "" ]]
2861    then
2862       echo  "$login_init_cmd"        >>  $jobfile
2863    fi
2864    if [[ "$module_commands" != "" ]]
2865    then
2866       echo  "$module_commands"     >>  $jobfile
2867    fi
2868
2869
2870       # CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
2871    if [[ $create_remote_batch_job = true ]]
2872    then
2873       echo  "mkdir  $tempdir"           >>  $jobfile
2874       echo  "chmod  go+rx  $tempdir"    >>  $jobfile
2875    else
2876          # DIRECTORY FOR LOCAL BATCH JOBS IS CREATED NOW, DUE TO A
2877          # REQUIREMENT OF THE GRID ENGINE BATCH SYSTEM (WORKING DIR IS GIVEN IN
2878          # BATCH DIRECTIVE -wd AND MUST ALREADY EXIST WHEN THE JOB IS SUBMITTED)
2879       mkdir  $tempdir
2880       chmod  go+rx  $tempdir
2881    fi
2882    echo  "cd  $tempdir"                 >>  $jobfile
2883    echo  "export tempdir=$tempdir"      >>  $jobfile
2884    echo  "cp  ${fast_io_catalog}/${sources_for_run_catalog}/{*,.[!.]*}  ."  >>  $jobfile
2885    echo  "export PATH=.:\$PATH"         >>  $jobfile
2886    echo  "export execute_palmrun=true"  >>  $jobfile
2887
2888
2889       # PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
2890       # STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN
2891       # IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
2892    echo  "LOCAL_PWD=$working_directory"                >>  $jobfile
2893    echo  "export LOCAL_PWD"                            >>  $jobfile
2894
2895
2896       # PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON
2897    echo  "LOCAL_PALMRUN_PATH=${source_path}/../SCRIPTS"   >>  $jobfile
2898    echo  "export LOCAL_PALMRUN_PATH"                      >>  $jobfile
2899
2900
2901       # CALL PALMRUN WITHIN THE JOB
2902       # AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
2903    echo  "set -x"                                              >>  $jobfile
2904    echo  "[[ \$execute_palmrun = true ]]  &&  $palmrun_com"    >>  $jobfile
2905
2906
2907       # TRANSFER JOBFILE TO THE TARGET HOST
2908    if [[ $create_jobfile_only = false ]]
2909    then
2910
2911       if [[ $create_remote_batch_job = true ]]
2912       then
2913
2914          echo " "
2915          echo " *** transfer of job to remote host via scp"
2916          if [[ $do_trace = true ]]
2917          then
2918             echo "     scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_configuration}_${job_id}"
2919          fi
2920          scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_configuration}_${job_id}  >  /dev/null
2921
2922          printf " *** submit the job (output of submit command, e.g. the job-id, may follow)"
2923          if [[ $do_trace = true ]]
2924          then
2925             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"
2926          fi
2927          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
2928
2929       elif [[ $create_batch_job = true ]]
2930       then
2931
2932          eval  local_jobcatalog=$local_jobcatalog
2933          cp  $jobfile  ${local_jobcatalog}/${host_configuration}_${job_id}
2934          cd $local_jobcatalog
2935          echo " "
2936          echo " *** submit the job"
2937          if [[ $do_trace = true ]]
2938          then
2939             echo "$submit_command ${host_configuration}_${job_id}"
2940          fi
2941          $submit_command ${host_configuration}_${job_id}
2942          rm ${host_configuration}_${job_id}
2943          cd -  > /dev/null
2944
2945       fi
2946
2947       rm -rf  $jobfile
2948
2949    else
2950
2951       printf "\n *** jobfile created under name \"$jobfile\" "
2952       printf "\n     no batch-job has been sent!"
2953
2954    fi
2955
2956 fi  # END OF REMOTE-PART
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