IJob.py 14.8 KB
Newer Older
eric pellegrini's avatar
test    
eric pellegrini committed
1
2
3
4
5
6
7
8
9
10
11
import abc
import glob
import os
import random
import stat
import string
import subprocess
import sys

from MDANSE import LOGGER, PLATFORM, REGISTRY
from MDANSE.Core.Error import Error
12
13
14
from MDANSE.Core.Configurable import Configurable
from MDANSE.Framework.Jobs.JobStatus import JobStatus
from MDANSE.Framework.OutputVariables.IOutputVariable import OutputData
eric pellegrini's avatar
test    
eric pellegrini committed
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29

class JobError(Error):
    pass

def key_generator(size=4, chars=None, prefix=""):
    
    if chars is None:
        chars = string.ascii_lowercase + string.digits
    
    key = ''.join(random.choice(chars) for _ in range(size))
    if prefix:
        key = "%s_%s" % (prefix,key)
    
    return key
        
30
class IJob(Configurable):
eric pellegrini's avatar
test    
eric pellegrini committed
31
    """
32
    This class handles a MDANSE job. In MDANSE any task modeled by a loop can be considered a MDANSE job. 
eric pellegrini's avatar
test    
eric pellegrini committed
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
    """
            
    __metaclass__ = REGISTRY
    
    type = "job"
    
    section = "job"
        
    @staticmethod
    def set_name():
        """
        Sets a name for the job that is not already in use by another running job.
        """
        
        prefix = '%d' % PLATFORM.pid()
    
        # The list of the registered jobs.
        registeredJobs = [os.path.basename(f) for f in glob.glob(os.path.join(PLATFORM.temporary_files_directory(),'*'))]
        
        while True:     
    
            # Followed by 4 random letters.
            name = key_generator(4, prefix=prefix)
            
            if not name in registeredJobs:
                break
                        
        return name
        
    def __init__(self, status=None):
        """
        The base class constructor.        
        """

        Configurable.__init__(self)
                
        self._outputData = OutputData()

71
        self._name = IJob.set_name()
eric pellegrini's avatar
test    
eric pellegrini committed
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
        
        self._info = ""
                                        
        if status is not None:
            self._status = JobStatus(self)
        else:
            self._status = None
                                
    def build_documentation(self):
                
        doc = [self.__doc__]
        for conf in self.configurators.values():
            if conf.__doc__ is None:
                doc.append("%s : %s\n" % (conf.type,'undocumented'))
            else:
                doc.append("%s : %s\n" % (conf.type,conf.__doc__))
                
        doc = '\n'.join(doc)
           
        return doc
    
    @classmethod
    def build_parallelization_test(cls, testFile, parameters=None):
        """
        Produce a file like object for a given job.\n
        :Parameters:
            #. parameters (dict): optional. If not None, the parameters with which the job file will be built.
        """
         
        # Try to open the output test file to see whether it is allowed.
        try:
            f = open(testFile, 'w')
        # Case where for whatever reason, the file could not be opened for writing. Return.        
        except IOError as e:
            raise JobError(["Error when saving python batch file.",e])
           
        # The first line contains the call to the python executable. This is necessary for the file to
        # be autostartable.
        f.write('#!%s\n\n' % sys.executable)

        f.write('import os\n')
        f.write('import unittest\n')
        f.write('import numpy\n')
        f.write('from Scientific.IO.NetCDF import NetCDFFile\n')
        f.write('from Tests.UnitTest import UnitTest\n')
117
        f.write('from MDANSE import REGISTRY\n\n')
eric pellegrini's avatar
test    
eric pellegrini committed
118
119
120
                
        f.write('class Test%sParallel(UnitTest):\n\n' % cls.type.upper())
        f.write('    def setUp(self):\n')
121
        f.write('        from MDANSE import LOGGER\n')
eric pellegrini's avatar
test    
eric pellegrini committed
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
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
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
        f.write('        LOGGER.stop()\n\n')
                    
        f.write('    def test(self):\n')      

        # Writes the line that will initialize the |parameters| dictionary.
        f.write('        parameters = {}\n')
        
        for k, v in sorted(parameters.items()):
            f.write('        parameters[%r] = %r\n' % (k, v))
                
        f.write('\n        job = REGISTRY[%r](%r)\n\n' % ('job',cls.type))

        f.write('        parameters["running_mode"] = ("monoprocessor",1)\n')
        f.write('        self.assertNotRaises(job.run,parameters,False)\n\n')

        f.write('        f = NetCDFFile(job.configuration["output_files"]["files"][0],"r")\n')
        f.write('        resMono = {}\n')
        f.write('        for k,v in f.variables.items():\n')
        f.write('            resMono[k] = v.getValue()\n')
        f.write('        f.close()\n\n')

        f.write('        parameters["running_mode"] = ("multiprocessor",2)\n')
        f.write('        self.assertNotRaises(job.run,parameters,False)\n\n')

        f.write('        f = NetCDFFile(job.configuration["output_files"]["files"][0],"r")\n')
        f.write('        resMulti = {}\n')
        f.write('        for k,v in f.variables.items():\n')
        f.write('            resMulti[k] = v.getValue()\n')
        f.write('        f.close()\n\n')

        f.write('        for k in resMono.keys():\n')
        f.write('            self.assertTrue(numpy.allclose(resMono[k],resMulti[k]))\n\n')
            
        f.write('def suite():\n')
        f.write('    loader = unittest.TestLoader()\n')
        f.write('    s = unittest.TestSuite()\n')
        f.write('    s.addTest(loader.loadTestsFromTestCase(Test%sParallel))\n' % cls.type.upper())
        f.write('    return s\n\n')
        f.write('if __name__ == "__main__":\n')
        f.write('    unittest.main(verbosity=2)\n')
        
        f.close()
        
        os.chmod(testFile,stat.S_IRWXU)

    @staticmethod
    def set_pyro_server():
    
        import Pyro.errors
        import Pyro.naming
    
        # Gets a Pyro proxy for the name server.
        locator = Pyro.naming.NameServerLocator()
    
        # Try to get an existing name server.        
        try:
            ns = locator.getNS()
            
        # Otherwise, start a new one.        
        except Pyro.errors.NamingError:
            
            subprocess.Popen([sys.executable, '-O', '-c', "import Pyro.naming; Pyro.naming.main([])"], stdout = subprocess.PIPE)
            ns = None
            while ns is None:
                try:
                    ns = locator.getNS()
                except Pyro.errors.NamingError:
                    pass
                            
    @property
    def name(self):
        return self._name

    @property
    def configuration(self):
        return self._configuration

    @abc.abstractmethod
    def finalize(self):        
        pass
        
    @abc.abstractmethod
    def initialize(self):        
        pass

    @abc.abstractmethod
    def run_step(self):
        pass
            
    @classmethod
    def save(cls, jobFile, parameters=None):
        """
        Save a job file for a given job.\n
        :Parameters:
            #. jobFile (str): The name of the output job file.\n
            #. parameters (dict): optional. If not None, the parameters with which the job file will be built.
        """
                         
        # Try to open the output job file to see whether it is allowed.
        try:
            f = open(jobFile, 'w')
        
        # Case where for whatever reason, the file could not be opened for writing. Return.        
        except IOError as e:
            raise JobError(["Error when saving python batch file.",e])
           
        # The first line contains the call to the python executable. This is necessary for the file to
        # be autostartable.
        f.write('#!%s\n\n' % sys.executable)
        
        # Writes the input file header.
        f.write('########################################################\n')
        f.write('# This is an automatically generated MDANSE run script #\n')
        f.write('#######################################################\n\n')
                                    
        # Write the import.
        f.write("from MDANSE import REGISTRY\n\n")
                        
        f.write('################################################################\n')
        f.write('# Job parameters                                               #\n')
        f.write('################################################################\n\n')

        # Writes the line that will initialize the |parameters| dictionary.
        f.write('parameters = {}\n')
        
        if parameters is None:
            parameters = cls.configurators.get_default_parameters()
        
        for k, v in sorted(parameters.items()):
            f.write('parameters[%r] = %r\n' % (k, v))

        f.write('\n')
        f.write('################################################################\n')
        f.write('# Setup and run the analysis                                   #\n')
        f.write('################################################################\n')
        f.write('\n')
    
        # Sets |analysis| variable to an instance analysis to save. 
        f.write('job = REGISTRY[%r][%r](status=False)\n' % ('job',cls.type))
        f.write('job.setup(parameters)\n')
        f.write('job.run()')
         
        f.close()
        
        os.chmod(jobFile,stat.S_IRWXU)
                
    @classmethod
    def build_test(cls, testFile, parameters=None):
        """
        Produce a file like object for a given job.\n
        :Parameters:
            #. parameters (dict): optional. If not None, the parameters with which the job file will be built.
        """
                
        # Try to open the output test file to see whether it is allowed.
        try:
            f = open(testFile, 'w')
        # Case where for whatever reason, the file could not be opened for writing. Return.        
        except IOError as e:
            raise JobError(["Error when saving python batch file.",e])
           
        # The first line contains the call to the python executable. This is necessary for the file to
        # be autostartable.
        f.write('#!%s\n\n' % sys.executable)

        f.write('import unittest\n')
        f.write('from Tests.UnitTest import UnitTest\n')
289
        f.write('from MDANSE import REGISTRY\n\n')
eric pellegrini's avatar
test    
eric pellegrini committed
290
291
292
                
        f.write('class Test%s(UnitTest):\n\n' % cls.type.upper())
        f.write('    def setUp(self):\n')
293
        f.write('        from MDANSE import LOGGER\n')
eric pellegrini's avatar
test    
eric pellegrini committed
294
295
296
297
298
299
300
        f.write('        LOGGER.stop()\n\n')
        
        f.write('    def test(self):\n')      

        # Writes the line that will initialize the |parameters| dictionary.
        f.write('        parameters = {}\n')
        
301
302
303
        if parameters is None:
            parameters = cls.configurators.get_default_parameters()
        
eric pellegrini's avatar
test    
eric pellegrini committed
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
        for k, v in sorted(parameters.items()):
            f.write('        parameters[%r] = %r\n' % (k, v))
    
        # Sets |analysis| variable to an instance analysis to save. 
        f.write('        job = REGISTRY[%r](%r)\n' % ('job',cls.type))
        f.write('        self.assertNotRaises(job.run, parameters,False)\n\n')
        
        f.write('def suite():\n')
        f.write('    loader = unittest.TestLoader()\n')
        f.write('    s = unittest.TestSuite()\n')
        f.write('    s.addTest(loader.loadTestsFromTestCase(Test%s))\n' % cls.type.upper())
        f.write('    return s\n\n')
        f.write("if __name__ == '__main__':\n")
        f.write('    unittest.main(verbosity=2)\n')
        
        f.close()
        
        os.chmod(testFile,stat.S_IRWXU)
        
    def _run_monoprocessor(self):

        if self._status is not None:
            self._status.start(self.numberOfSteps,rate=0.1)

        for index in range(self.numberOfSteps):
            idx, x = self.run_step(index)                            
            self.combine(idx, x)
            
            if self._status is not None:
                if self._status.is_stopped():
                    self._status.cleanup()
                    return
                else:
                    self._status.update()
        
    def _run_multiprocessor(self):

        import MDANSE.DistributedComputing.MasterSlave as MasterSlave

        script = os.path.abspath(os.path.join(PLATFORM.package_directory(),'DistributedComputing','Slave.py'))
                
        master = MasterSlave.initializeMasterProcess(self._name, slave_script=script, use_name_server=False)

        master.setGlobalState(job=self)
        master.launchSlaveJobs(n=self.configuration['running_mode']['slots'],port=master.pyro_daemon.port)

        if self._status is not None:
            self._status.start(self.numberOfSteps,rate=0.1)

        for index in range(self.numberOfSteps):
            master.requestTask('run_step',MasterSlave.GlobalStateValue(1,'job'),index)
        
        for index in range(self.numberOfSteps):
            _, _, (idx, x) = master.retrieveResult('run_step')
            self.combine(idx, x)

            if self._status is not None:
                if self._status.is_stopped():
                    self._status.cleanup()
                    return
                else:
                    self._status.update()
            
        master.shutdown()
        
    def _run_remote(self):

371
        IJob.set_pyro_server()
eric pellegrini's avatar
test    
eric pellegrini committed
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420

        import MDANSE.DistributedComputing.MasterSlave as MasterSlave

        tasks = MasterSlave.initializeMasterProcess(self._name, slave_module='MDANSE.DistributedComputing.Slave')
             
        tasks.setGlobalState(job=self)

        if self._status is not None:
            self._status.start(self.numberOfSteps,rate=0.1)
                
        for  index in range(self.numberOfSteps):
            tasks.requestTask('run_step',MasterSlave.GlobalStateValue(1,'job'),index)

        for index in range(self.numberOfSteps):
            _, _, (idx, x) = tasks.retrieveResult("run_step")
            self.combine(idx, x)

        if self._status is not None:
            if self._status.is_stopped():
                self._status.cleanup()
                return
            else:
                self._status.update()
            
    _runner = {"monoprocessor" : _run_monoprocessor, "multiprocessor" : _run_multiprocessor, "remote" : _run_remote}

    def run(self, parameters=None):
        """
        Run the job.
        """
        
        if parameters is not None:
            self.setup(parameters)
        
        self.initialize()

        self._info = 'Information about %s job.\n' % self._name
        self._info += str(self)
                                                  
        LOGGER(self._info)
                  
        if getattr(self,'numberOfSteps', 0) <= 0:
            raise JobError("Invalid number of steps for job %s" % self)

        try:
            mode = self.configuration['running_mode']['mode']
        except:
            raise JobError("Invalid running mode")
        else:                        
421
            IJob._runner[mode](self)
eric pellegrini's avatar
test    
eric pellegrini committed
422
423
424
425
426
427
428
429
430
431

        self.finalize()

        if self._status is not None:
            self._status.finish()

    @property
    def info(self):
            
        return self._info