initexit.py 30 KB
Newer Older
1
2
3
4
#!/usr/bin/env python
# da_initexit.py

"""
Peters, Wouter's avatar
Peters, Wouter committed
5
6
.. module:: initexit
.. moduleauthor:: Wouter Peters 
7
8
9
10

Revision History:
File created on 13 May 2009.

Peters, Wouter's avatar
Peters, Wouter committed
11
The CycleControl class is found in the module :mod:`initexit`. It is derived from the standard python :class:`dictionary` object. It is the only core object of CTDAS that is automatically created in the pipeline, the user (normally) does not need to modify or extend it. The class is created based on options and arguments passes on the command line when submitting your main CTDAS job. 
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43

Valid options are defined in 

.. autofunction:: da.tools.initexit.ParseOptions

With the name of a valid ``rc-file``, the CycleControl object is instantiated and validated. An example rc-file looks
like this:::

    ! Info on the data assimilation cycle

    time.restart        : False
    time.start          : 2000-01-01 00:00:00
    time.finish         : 2000-01-08 00:00:00
    time.cycle          : 7
    time.nlag           : 2
    dir.da_run          : ${HOME}/tmp/test_da

    ! Info on the DA system used

    da.system           : CarbonTracker
    da.system.rc        : carbontracker.rc
    da.platform         : maunaloa

    ! Info on the forward model to be used

    forecast.model      : TM5
    forecast.model.rc   : ${HOME}/Modeling/TM5/ct_new.rc
    forecast.nmembers   : 2

The most important method of the CycleControl object are listed below:

.. autoclass:: da.tools.initexit.CycleControl 
44
45
   :members: Initialize, Finalize,  CollectRestartData, MoveRestartData, 
             SubmitNextCycle, CleanUpCycle, SetupFileStructure, RecoverRun, RandomSeed
46
47
48
49
50
51
52
53
54
55
56

Two important attributes of the CycleControl object are:
    (1) DaSystem, an instance of a :ref:`dasystem`
    (2) DaPlatForm, an instance of a :ref:`platform`

Other functions in the module initexit that are related to the control of a DA cycle are:

.. autofunction:: da.tools.initexit.StartLogger 
.. autofunction:: da.tools.initexit.ValidateOptsArgs 


57
58
59
60
61
62
63
64
"""

needed_da_items=[
    'time.start',
    'time.finish',
    'time.nlag',
    'time.cycle',
    'dir.da_run',
65
    'forecast.nmembers']
66
67
68
69
70
71
72
73
74
75
76
77
78
79

# only needed in an earlier implemented where each substep was a separate job
# validprocesses = ['start','done','samplestate','advance','invert']

import logging
import os
import sys
import shutil
import datetime



class CycleControl(dict):
    """
80
    This object controls the CTDAS system flow and functionality.
81
    """
82
83
        
    def __init__(self,opts=[],args={}):
84
        """
Peters, Wouter's avatar
Peters, Wouter committed
85
86
87
88
        The CycleControl object is instantiated with a set of options and arguments.
        The list of arguments must contain the name of an existing ``rc-file``. 
        This rc-file is loaded by method :meth:`~da.tools.initexit.CycleControl.LoadRc` and validated
        by :meth:`~da.tools.initexit.CycleControl.ValidateRC`
89

Peters, Wouter's avatar
Peters, Wouter committed
90
91
        Options for the CycleControl consist of accepted command line flags or arguments 
        in :func:`~da.tools.initexit.CycleControl.ParseOptions`
92

93
94
95
96
97
98
99
100
101
102
103
104
105
        """

        self.LoadRc(args['rc'])
        self.ValidateRC()
        self.opts = opts

        # Add some useful variables to the rc-file dictionary

        self['jobrcfilename']    = self.RcFileName
        self['dir.da_submit']    = os.getcwd()
        self['da.crash.recover'] = '-r' in opts
        self['verbose']          = '-v' in opts
        self.DaSystem            = None # to be filled later
106
        self.RestartFileList     = [] # List of files needed for restart, to be extended later
107
        self.OutputFileList      = () # List of files needed for output, to be extended later
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127

    def __str__(self):
        """
        String representation of a CycleControl object
        """

        msg = "==============================================================="    ; print msg
        msg = "DA Cycle rc-file is %s" % self.RcFileName                                ; print msg
        msg = "DA Cycle run directory is %s" % self['dir.da_run']           ; print msg
        msg = "DA Cycle inverse system is %s" % self['da.system']           ; print msg
        msg = "DA Cycle forecast model is %s" % self['forecast.model']      ; print msg
        msg = "==============================================================="    ; print msg

        return ""


    def LoadRc(self,RcFileName):
        """ 
        This method loads a DA Cycle rc-file with settings for this simulation 
        """
128
        import da.tools.rc as rc
129
130
131
132
133
134
135
136
137
138
139
140
141
142

        rcdata = rc.read(RcFileName)
        for k,v in rcdata.iteritems():
            self[k] = v
        self.RcFileName     = RcFileName
        self.DaRcLoaded    = True

        msg                 = 'DA Cycle rc-file (%s) loaded successfully'%self.RcFileName ; logging.info(msg)

        return True


    def ValidateRC(self):
        """ 
Peters, Wouter's avatar
Peters, Wouter committed
143
144
        Validate the contents of the rc-file given a dictionary of required keys. 
        Currently required keys are :attr:`~da.tools.initexit.needed_da_items`
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
        """
        from da.tools.general import ToDatetime

        for k,v in self.iteritems():
            if v == 'True' : self[k] = True
            if v == 'False': self[k] = False
            if 'date' in k : self[k] = ToDatetime(v)
            if 'time.start' in k : 
                self[k] = ToDatetime(v)
            if 'time.end' in k : 
                self[k] = ToDatetime(v)
            if 'time.finish' in k : 
                self[k] = ToDatetime(v)

        for key in needed_da_items:

            if not self.has_key(key):
                status,msg = ( False,'Missing a required value in rc-file : %s' % key)
                logging.error(msg)
                raise IOError,msg

        status,msg = ( True,'DA Cycle settings have been validated succesfully' )  ; logging.debug(msg)

        return None

    def ParseTimes(self):
        """ 
        Parse time related parameters into datetime objects for later use 
        """
        from da.tools.general import AdvanceTime

        startdate = self['time.start']
        finaldate = self['time.finish']                  

        if finaldate <= startdate:
            msg   = 'The start date (%s) is not greater than the end date (%s), please revise'%(startdate.strftime('%Y%m%d'),finaldate.strftime('%Y%m%d')) 
            logging.error(msg)
            raise ValueError
        #
        cyclelength = self['time.cycle']                 # get time step

# Determine end date

        if cyclelength == 'infinite':
            enddate = finaldate
        else:
            enddate = AdvanceTime(startdate,cyclelength)

        #
        if enddate > finaldate:  # do not run beyon finaldate
            enddate = finaldate

        self['time.start']   = startdate
        self['time.end']     = enddate
        self['time.finish']  = finaldate
        self['cyclelength']  = cyclelength

        msg = "==============================================================="    ; logging.info(msg)
        msg = "DA Cycle start date is %s"   % startdate.strftime('%Y-%m-%d %H:%M')      ; logging.info(msg)
        msg = "DA Cycle end   date is %s"   % enddate.strftime('%Y-%m-%d %H:%M')        ; logging.info(msg)
        msg = "DA Cycle final date is %s"   % finaldate.strftime('%Y-%m-%d %H:%M')      ; logging.info(msg)
        msg = "DA Cycle cycle length is %s" % cyclelength                               ; logging.info(msg)
        msg = "DA Cycle restart is %s"      % str(self['time.restart'])     ; logging.info(msg)
        msg = "==============================================================="    ; logging.info(msg)

        return None

    def RandomSeed(self,action='read'):
Peters, Wouter's avatar
Peters, Wouter committed
213
214
        """ 
        Get the randomseed and save it, or read the random seed and set it. The seed is currently stored
215
        in a python :mod:`pickle` file, residing in the ``exec`` directory
Peters, Wouter's avatar
Peters, Wouter committed
216
217

        """
218
219
220
        import cPickle
        import numpy as np

221
        filename = os.path.join(self['dir.exec'],'randomseed.pickle')
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240

        if action == 'write':
            f        = open(filename,'wb')
            seed     = np.random.get_state()
            dummy    = cPickle.dump (seed,f,-1)
            dummy    = f.close()

            msg      = "Saved the random seed generator values to file"

        if action == 'read':
            f        = open(filename,'rb')
            seed     = cPickle.load(f)
            dummy    = np.random.set_state(seed)
            dummy    = f.close()

            msg      = "Retrieved the random seed generator values from file"

        logging.info(msg)

241
242
243
244
245
        dummy    = self.RestartFileList.append(filename)

        msg      = "Added the randomseed.pickle file to the RestartFileList" ; logging.debug(msg)


246
247
248
        return None

    def Initialize(self):
249
250
251
        """ 
        This method determines how to proceed with the cycle. Three options are implemented:

Peters, Wouter's avatar
Peters, Wouter committed
252
253
254
            1. *Fresh start*  : set up the required file structure for this simulation and start
            2. *Restart*      : use latest da_runtime variables from the exec dir and restart
            3. *Recover*      : restart after crash by getting data from restart/one-ago folder
255
256
257

        The choice that gets executed depends on the presence of 

Peters, Wouter's avatar
Peters, Wouter committed
258
259
            # the ``-r`` option on the command line, this triggers a recover
            # the ``time.restart : True`` option in the da.rc file
260
261

        The latter is automatically set if the filter submits the next cycle at the end of the current one, 
Peters, Wouter's avatar
Peters, Wouter committed
262
263
        through method :meth:`~da.tools.initexit.CycleControl.SubmitNextCycle`.

Peters, Wouter's avatar
Peters, Wouter committed
264
        The specific call tree under each scenario is: 
Peters, Wouter's avatar
Peters, Wouter committed
265

Peters, Wouter's avatar
Peters, Wouter committed
266
            1. *Fresh Start*
Peters, Wouter's avatar
Peters, Wouter committed
267
                * dummy = :meth:`~da.tools.initexit.CycleControl.SetupFileStructure()`  <- Create directory tree
Peters, Wouter's avatar
Peters, Wouter committed
268
            2. *Restart*
Peters, Wouter's avatar
Peters, Wouter committed
269
270
                * dummy = :meth:`~da.tools.initexit.CycleControl.SetupFileStructure()`
                * dummy = :meth:`~da.tools.initexit.CycleControl.RandomSeed`    <- Read the random seed from file
Peters, Wouter's avatar
Peters, Wouter committed
271
            3. *Recover*
Peters, Wouter's avatar
Peters, Wouter committed
272
                * dummy = :meth:`~da.tools.initexit.CycleControl.SetupFileStructure()`
273
                * dummy = :meth:`~da.tools.initexit.CycleControl.RecoverRun()`          <- Recover files from restart/one-ago dir, reset ``time.start``
Peters, Wouter's avatar
Peters, Wouter committed
274
275
276
277
                * dummy = :meth:`~da.tools.initexit.CycleControl.RandomSeed` 

        And is always followed by a call to

Peters, Wouter's avatar
Peters, Wouter committed
278
279
            * ParseTimes()
            * WriteRc('jobfilename')
Peters, Wouter's avatar
Peters, Wouter committed
280

281

282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
        """        

#
# case 1: A recover from a previous crash, this is signaled by flag "-r"
#
        if self['da.crash.recover']:

            msg   = "Recovering simulation from data in: %s" % self['dir.da_run']  ; logging.info(msg)

            dummy = self.SetupFileStructure()

            dummy = self.RecoverRun()

            dummy = self.RandomSeed('read')
#
# case 2: A continuation, this is signaled by rc-item time.restart = True
#
        elif self['time.restart']:

            msg   = "Restarting filter from previous step"  ; logging.info(msg)

            dummy = self.SetupFileStructure()

            dummy = self.RandomSeed('read')
#
# case 3: A fresh start, this is signaled by rc-item time.restart = False
#
        elif not self['time.restart']:
            msg   = "First time step in filter sequence"   ; logging.info(msg)

            dummy = self.SetupFileStructure()

            # expand jobrcfilename to include exec dir from now on.

            self['jobrcfilename'] = os.path.join(self['dir.exec'],self['jobrcfilename'])


        self.ParseTimes()
        self.WriteRC(self['jobrcfilename'])

        return None


    def SetupFileStructure(self):
        """ 
        Create file structure needed for data assimilation system.
Peters, Wouter's avatar
Peters, Wouter committed
328
329
330
331
332
333
334
335
336
        In principle this looks like:

            * ``${da_rundir}``
            * ``${da_rundir}/input``
            * ``${da_rundir}/output``
            * ``${da_rundir}/exec``
            * ``${da_rundir}/diagnostics``
            * ``${da_rundir}/analysis``
            * ``${da_rundir}/jobs``
337
338
            * ``${da_rundir}/restart/current``
            * ``${da_rundir}/restart/one-ago``
Peters, Wouter's avatar
Peters, Wouter committed
339

340
        .. note:: The exec dir will actually be a simlink to the directory where
341
342
343
                 the observation operator executable lives. This directory is passed through
                 the ``da.rc`` file. 

344
        .. note:: The observation input files will be placed in the exec dir,
345
                 and the resulting simulated values will be retrieved from there as well.
Peters, Wouter's avatar
Peters, Wouter committed
346

347
348
349
350
351
352
353
354
355
356
357
358
359
        """
        from da.tools.general import CreateDirs

# Create the run directory for this DA job, including I/O structure

        filtertime  = self['time.start'].strftime('%Y%m%d')

        self['dir.exec']        = os.path.join(self['dir.da_run'],'exec')
        self['dir.input']       = os.path.join(self['dir.da_run'],'input')
        self['dir.output']      = os.path.join(self['dir.da_run'],'output',filtertime)
        self['dir.diagnostics'] = os.path.join(self['dir.da_run'],'diagnostics')
        self['dir.analysis']    = os.path.join(self['dir.da_run'],'analysis')
        self['dir.jobs']        = os.path.join(self['dir.da_run'],'jobs')
360
361
362
        self['dir.restart']     = os.path.join(self['dir.da_run'],'restart')
        self['dir.restart.current']    = os.path.join(self['dir.restart'],'current')
        self['dir.restart.oneago']     = os.path.join(self['dir.restart'],'one-ago')
363
364
365
366
367
368
369
370

        CreateDirs(self['dir.da_run'])
        CreateDirs(os.path.join(self['dir.exec']))
        CreateDirs(os.path.join(self['dir.input']))
        CreateDirs(os.path.join(self['dir.output']))
        CreateDirs(os.path.join(self['dir.diagnostics']))
        CreateDirs(os.path.join(self['dir.analysis']))
        CreateDirs(os.path.join(self['dir.jobs']))
371
372
373
        CreateDirs(os.path.join(self['dir.restart']))
        CreateDirs(os.path.join(self['dir.restart.current']))
        CreateDirs(os.path.join(self['dir.restart.oneago']))
374
375
376
377
378

        msg = 'Succesfully created the file structure for the assimilation job'  ; logging.info(msg)


    def RecoverRun(self):
Peters, Wouter's avatar
Peters, Wouter committed
379
380
        """
        Prepare a recovery from a crashed run. This consists of: 
381
        
382
            - copying all data from the restart/one-ago folder (:meth:`~da.tools.initexit.CycleControl.MoveRestartData`),
383
            - replacing all ``rc-file`` items with those from the ``da_runtime.rc`` in the restart/current dir 
Peters, Wouter's avatar
Peters, Wouter committed
384
            - resetting the seed of the random number generator to the value it had before the crash (:meth:`~da.tools.initexit.CycleControl.RandomSeed`)
385
            - replacing the output dir name, since it has the sample time in it...
Peters, Wouter's avatar
Peters, Wouter committed
386
            
387
        """
388
389
        import da.tools.rc as rc
        import shutil
390
        from da.tools.general import CreateDirs
391

392
        # Replace rc-items with those from the crashed run's last rc-file (now in restart.current dir)
393

394
        file_rc_rec = os.path.join(self['dir.restart.current'],'da_runtime.rc')
395
396
397
398
399
400
401
        rc_rec      = rc.read(file_rc_rec)

        for k,v in rc_rec.iteritems():
            self[k] = v

        self.ValidateRC()

402
        msg         = "Replaced rc-items.... "                            ; logging.debug(msg)
403
404
        msg         = "Next cycle start date is %s" % self['time.start']  ; logging.debug(msg)

405
406
407
408
409
410
411
412
        # Copy randomseed.pickle file to exec dir

        source        = os.path.join(self['dir.restart.current'],'randomseed.pickle')
        dest          = os.path.join(self['dir.exec'],'randomseed.pickle')
        dummy         = shutil.copy(source,dest)

        msg           = "Replaced randomseed file with previous cycles' last values"          ; logging.debug(msg)

413
414
415
416
417
418
        # Re-create the output dir for this time step, if needed

        filtertime  = self['time.start'].strftime('%Y%m%d')
        self['dir.output']      = os.path.join(self['dir.da_run'],'output',filtertime)
        CreateDirs(os.path.join(self['dir.output']))

419
420
421
422
        return None

    def Finalize(self):
        """
423
424
425
426
        Finalize the da cycle, this means writing the save data and rc-files for the next run. 
        The following sequence of actions occur:

            * Write the randomseed to file for reuse in next cycle
Peters, Wouter's avatar
Peters, Wouter committed
427
            * Write a new ``rc-file`` with ``time.restart : True``, and new ``time.start`` and ``time.end``
428
429
430
431
            * Collect all needed data needed for check-pointing (restart from current system state)
            * Move the previous check pointing data out of the way, and replace with current
            * Submit the next cycle

432
433
434
435
        """

        dummy = self.RandomSeed('write')
        dummy = self.WriteNewRCfile()
436
437
        dummy = self.MoveRestartData(io_option='store')  # Move restart data from current to one-ago
        dummy = self.CollectRestartData()  # Collect restart data for next cycle into a clean restart/current folder
438
        dummy = self.CollectOutput()  # Collect restart data for next cycle into a clean restart/current folder
439
440
        dummy = self.SubmitNextCycle()

441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
    def CollectOutput(self):
        """ Collect files that are vpart of the requested output for this cycle. This function allows users to add files 
            to a list, and then the system will copy these to the current cycle's output directory.
            The list of files included is read from the 
            attribute "OutputFileList" which is a simple list of files that can be appended by other objects/methods that
            require output data to be saved.


        """
        from da.tools.general import CreateDirs

        targetdir   = os.path.join(self['dir.output'])

        CreateDirs(os.path.join(targetdir) )

        msg         = "Collecting the required output data"                                       ; logging.info(msg)
        msg         = "           to   directory: %s " % targetdir                                ; logging.debug(msg)

        for file in set(self.OutputFileList):

            if os.path.isdir(file): # skip dirs
                continue
463
464
465
            if not os.path.exists(file): # skip dirs
                msg         = "           [not found] .... %s " % file                                     ; logging.warning(msg)
                continue
466
467
468
469
470
471

            msg         = "           [copy] .... %s " % file                                     ; logging.debug(msg)
            dummy       = shutil.copy(file,file.replace(os.path.split(file)[0],targetdir) )



472
    def CollectRestartData(self):
473
        """ Collect files needed for the restart of this cycle in case of a crash, or for the continuation of the next cycle. 
474
            All files needed are written to the restart/current directory. The list of files included is read from the 
475
476
477
            attribute "RestartFileList" which is a simple list of files that can be appended by other objects/methods that
            require restart data to be saved.

478
            .. note:: Before collecting the files in the ``RestartFileList``, the restart/current directory will be emptied and
479
480
481
482
483
                     recreated. This prevents files from accumulating in the restart/current and restart/one-ago folders. It 
                     also means that if a file is missing from the ``RestartFileList``, it will not be available for check-pointing
                     if your run crashes or dies!

            Currently, the following files are included:
484

485
                * The ``da_runtime.rc`` file
486
                * The ``randomseed.pickle`` file
487
488
                * The savestate.nc file
                * The files in the ``ObservationOperator.RestartFileList``, i.e., restart data for the transport model
489

490

Peters, Wouter's avatar
Peters, Wouter committed
491
            .. note:: We assume that the restart files for the :ref:`ObservationOperator` 
492
                      reside in a separate folder, i.e, the ObservationOperator does *not* write directly to the CTDAS restart dir!
493
494

        """
495
        from da.tools.general import CreateDirs
496

497
        targetdir   = os.path.join(self['dir.restart.current'])
498

499
500
501
502
        msg         = "Purging the current restart directory before collecting new data"         ; logging.info(msg)

        CreateDirs(os.path.join(targetdir),forceclean=True)

503
        msg         = "Collecting the required restart data"                                      ; logging.info(msg)
504
505
        msg         = "           to   directory: %s " % targetdir                                ; logging.debug(msg)

506

507
        for file in set(self.RestartFileList):
508
509
510

            if os.path.isdir(file): # skip dirs
                continue
511
512
513
514
515

            msg         = "           [copy] .... %s " % file                                     ; logging.debug(msg)
            dummy       = shutil.copy(file,file.replace(os.path.split(file)[0],targetdir) )


516
    def MoveRestartData(self, io_option='restore'):
Peters, Wouter's avatar
Peters, Wouter committed
517
        """ 
518
        Store or restore model state to/from a restart directory. 
519

520
            Two IO options are available:
521

522
523
            (1) io_option = restore    : Get data from restart.oneago directory
            (2) io_option = store      : Save data to restart.oneago directory
524

525
            In case of a 'store' command the restart.oneago folder is re-created so that the contents are empty to begin with.
526
527
528
529
530
531
532

        """
        from da.tools.general import CreateDirs

        if io_option not in ['store','restore']:
            raise ValueError,'Invalid option specified for io_option (%s)' % io_option

533
        if io_option == 'store':
534

535
536
            targetdir = self['dir.restart.oneago']
            sourcedir = self['dir.restart.current']
537

538
        elif io_option == 'restore':
539

540
541
            sourcedir = self['dir.restart.oneago']
            targetdir = self['dir.restart.current']
542
543
544
545
546
547

# If "store" is requested, recreate target dir, cleaning the contents 

        if io_option == 'store':
            CreateDirs(os.path.join(targetdir),forceclean=True)

548
        msg         = "Performing a %s of data" % (io_option)                                     ; logging.debug(msg)
549
550
551
552
553
554
555
556
557
        msg         = "           from directory: %s " % sourcedir                                ; logging.debug(msg)
        msg         = "           to   directory: %s " % targetdir                                ; logging.debug(msg)


        for file in os.listdir(sourcedir):

            file = os.path.join(sourcedir,file)

            if os.path.isdir(file): # skip dirs
558

559
560
                msg         = "           [skip] .... %s " % file                                     ; logging.debug(msg)
                continue    
561
            else:
562
563
564
565
566
567

                msg         = "           [copy] .... %s " % file                                                ; logging.debug(msg)
                dummy       = shutil.copy(file,file.replace(sourcedir,targetdir) )

#
    def WriteNewRCfile(self):
568
569
570
571
572
573
        """ Write the rc-file for the next DA cycle. 

            .. note:: The start time for the next cycle is the end time of this one, while 
                      the end time for the next cycle is the current end time + one cycle length. 
                      
            The resulting rc-file is written to the ``dir.exec`` so that it can be used when resubmitting the next cycle
574
575
576
            
        """
        from da.tools.general import AdvanceTime
577
        import da.tools.rc as rc
578
579
580
581
582
583
584
585
586
587
588
589
590

        # These first two lines advance the filter time for the next cycle

        self['time.start']        = self['time.end']
        self['time.end']          = AdvanceTime(self['time.end'],self['cyclelength'])

        # The rest is info needed for a system restart

        self['time.restart']     = True
        #self['time.start']       = self['time.start'].strftime('%Y-%m-%d %H:%M:%S')
        #self['time.finish']      = self['time.finish'].strftime('%Y-%m-%d %H:%M:%S')

        fname                                = os.path.join(self['dir.exec'],'da_runtime.rc')
591
        self['da.restart.fname']             = fname
592
593
        dummy                                = rc.write(fname,self)

594
595
596
597
        dummy                                = self.RestartFileList.append(fname)

        msg = 'Added da_runtime.rc to the RestartFileList for later collection' ; logging.debug(msg)
        msg = 'Wrote new da_runtime.rc (%s) to exec dir'%fname ; logging.debug(msg)
598
599
600
601


    def WriteRC(self,fname):
        """ Write RC file after each process to reflect updated info """
602
        import da.tools.rc as rc
603
604
605
606
607
608
609

        dummy  = rc.write(fname,self)
        msg    = 'Wrote expanded rc-file (%s)'%(fname) ; logging.debug(msg)
        return None

    def SubmitNextCycle(self):
        """ 
Peters, Wouter's avatar
Peters, Wouter committed
610
        Submit the next job of a DA cycle, this consists of 
611
612
613
            * Changing to the working directory from which the job was started initially
            * create a line to start the master script again with a newly created rc-file
            * Submitting the jobfile 
Peters, Wouter's avatar
Peters, Wouter committed
614
615
616

        If the end of the cycle series is reached, no new job is submitted.

617
618
619
        """
        import subprocess
        import os
620
        from string import join
621
622
623
624
625
626


        DaPlatForm = self.DaPlatForm

        if self['time.start'] < self['time.finish']:

627
            jobparams               = {'jobname':sys.argv[0][2:],'jobtime':'01:30:00'}
628
            template                = DaPlatForm.GetJobTemplate(jobparams)
629
            jobcommand              = '%s rc=%s'% (sys.argv[0], self['da.restart.fname'], ) 
630
            template                += 'cd %s\n'% self['dir.da_submit'] 
631
            template                += 'rm -f core.*\n'
632
            template                += '%s rc=%s %s' % (sys.argv[0],self['da.restart.fname'],join(self.opts,''),) 
633
634
            jobfile                 = DaPlatForm.WriteJob(self,template,self['time.start'].strftime('%Y%m%d') )
            jobid                   = DaPlatForm.SubmitJob(jobfile) 
635
636
637
638
639
640
        else:
            logging.info('Final date reached, no new cycle started')

        return None

    def SubmitSubStep(self,stepname):
Peters, Wouter's avatar
Peters, Wouter committed
641
642
643
644
645
646
647
648
        """ 
        Submit the next substep of a DA cycle, this consists of 
            * getting a job template as returned by :meth:`~da.tools.baseclasses.platform.GetJobTemplate`
            * adding the lines needed to start a next run with a newly created rc-file
            * Writing the jobfile as done by :meth:`~da.tools.baseclasses.platform.WriteJob`
            * Submitting the jobfile as done by :meth:`~da.tools.baseclasses.platform.WriteJob`

        """
649
650
651
652
653
654
655
656
657
658
        import subprocess
        import os
        from string import join


        DaPlatForm = self.DaPlatForm

        jobparams               = {'jobname':'das.%s'%stepname}
        template                = DaPlatForm.GetJobTemplate(jobparams)
        template                += 'cd %s\n'%os.getcwd()
659
        template                += '%s rc=%s process=%s %s' % (sys.argv[0],self['jobrcfilename'],stepname,join(self.opts,''),) 
660
661
662
663
664
        jobfile                 = DaPlatForm.WriteJob(self,template,stepname)
        jobid                   = DaPlatForm.SubmitJob(jobfile) 

        return None

665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
    def CleanUpCycle(self):
        """
        Move the log file, clean up rundir after a cycle has finished
        """

        # move log file to rundir/jobs
        jobdir      = os.path.join(self['dir.da_run'],"jobs")
        logfile     = 'das.o%s'%self.DaPlatForm.GetMyID()

        if os.path.exists(logfile):
            joblogfile  = os.path.join(jobdir,'cycle.%s.log'%self['time.sample.start'].strftime('%Y%m%d')) 
            dummy       = shutil.move(logfile,joblogfile)
            msg         = "....Moved %s to %s"%(logfile,joblogfile)   ; logging.debug(msg)

            msg = "The complete log file is now at: %s"%(joblogfile)   ; logging.info(msg)


682
683
684
685
686
687
688
689
690
691
692

def StartLogger():
    """ start the logging of messages to screen"""

# start the logging basic configuration by setting up a log file

    logging.basicConfig(level    = logging.INFO,
                        format   = ' [%(levelname)-7s] (%(asctime)s) py-%(module)-20s : %(message)s',
                        datefmt  = '%Y-%m-%d %H:%M:%S')

def ParseOptions():
693
694
695
696
697
698
699
700
701
702
703
704
705
    """ 
    Function parses options from the command line and returns the arguments as a dictionary.
    Accepted command line arguments are:

    ========  =======
    Argument  Meaning
    ========  =======
    -v        verbose output in log files
    -h        display help
    -r        start a simulation by recovering from a previous crash
    ========  =======

    """
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
    import getopt
    import sys

# Parse keywords, the only option accepted so far is the "-h" flag for help

    opts=[]
    args=[]
    try:                                
        opts, args = getopt.gnu_getopt(sys.argv[1:], "-hrv")
    except getopt.GetoptError, msg:           
        logging.error('%s'%msg)
        sys.exit(2)      

    for options in opts:
        options=options[0].lower()
        if options == '-h':
            print ""
            print helptext
            sys.exit(2)      
        if options == '-r':
            logging.info('-r flag specified on command line: recovering from crash')
        if options == '-v':
            logging.info('-v flag specified on command line: extra verbose output')
            dummy  = logging.root.setLevel(logging.DEBUG)

731
732
733
734
735
    if opts: 
        optslist=[item[0] for item in opts]
    else:
        optslist=[]

736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
# Parse arguments and return as dictionary

    arguments={}
    for item in args:
        #item=item.lower()

# Catch arguments that are passed not in "key=value" format

        if '=' in item:
            key, arg = item.split('=')
        else:
            logging.error('%s'%'Argument passed without description (%s)' % item)
            raise getopt.GetoptError,arg

        arguments[key]=arg


753
    return optslist, arguments
754
755

def ValidateOptsArgs(opts,args):
756
757
758
759
760
    """ 
 Validate the options and arguments passed from the command line before starting the cycle. The validation consists of checking for the presence of an argument "rc", and the existence of
 the specified rc-file.  
 
    """
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780

    if not args.has_key("rc"):
        msg = "There is no rc-file specified on the command line. Please use rc=yourfile.rc"   ; logging.error(msg)
        raise IOError,msg
    elif not os.path.exists(args['rc']):
        msg = "The specified rc-file (%s) does not exist " % args['rc'] ;  logging.error(msg)
        raise IOError,msg

    # WP not needed anymore
    #if not args.has_key('process'):
    #    msg = "There is no process specified on the command line, assuming process=Start"   ; logging.info(msg)
    #    args['process'] = 'start'
    #if args['process'].lower() not in validprocesses:
    #    msg = "The specified process (%s) is not valid"%args['process']   ; logging.error(msg)
    #    raise IOError,msg

    return opts,args


if __name__ == "__main__":
781
782
783
784
785

    sys.path.append('../../')
    opts,args = ParseOptions()
    print opts
    print args
786