Beispiel #1
0
    def __init__(self, task):
        self.use_load_balancing = not task.get_custom_field('skip_load_balancing_step')

        if self.use_load_balancing:
            self.subtasks = 3
        else:
            self.subtasks = 2
            task.set_custom_field('repeats_per_job', 1)
            task.save()
            
        super(TaskPlugin, self).__init__(task)
        self.copasi_model = PSCopasiModel(os.path.join(self.task.directory, self.task.original_model))
Beispiel #2
0
    def __init__(self, task):
        self.use_load_balancing = not task.get_custom_field('skip_load_balancing_step')

        if self.use_load_balancing:
            self.subtasks = 3
        else:
            self.subtasks = 2
            task.set_custom_field('repeats_per_job', 1)
            task.save()
            
        super(TaskPlugin, self).__init__(task)
        self.copasi_model = PSCopasiModel(os.path.join(self.task.directory, self.task.original_model))
Beispiel #3
0
class TaskPlugin(BaseTask):

    subtasks = 3

    def __init__(self, task):
        self.use_load_balancing = not task.get_custom_field(
            'skip_load_balancing_step')

        if self.use_load_balancing:
            self.subtasks = 3
        else:
            self.subtasks = 2
            task.set_custom_field('repeats_per_job', 1)
            task.save()

        super(TaskPlugin, self).__init__(task)
        self.copasi_model = PSCopasiModel(
            os.path.join(self.task.directory, self.task.original_model))

    def validate(self):
        #TODO:Abstract this to a new COPASI class in this plugin package
        return self.copasi_model.is_valid('PS')

    def initialize_subtasks(self):
        #Create new subtask objects, and save them
        if self.use_load_balancing:
            #Create the load balancing module
            self.create_new_subtask('lb')

        #The main module
        self.create_new_subtask('main')
        #And a subtask to process any results
        self.create_new_subtask('process', local=True)

    def prepare_subtask(self, index):
        """Prepare the indexed subtask"""

        if index == 1:
            if self.use_load_balancing:
                return self.process_lb_subtask()
            else:
                return self.process_main_subtask()

        elif index == 2:
            if self.use_load_balancing:
                return self.process_main_subtask()
            else:
                return self.process_results_subtask()
        elif index == 3:
            assert self.use_load_balancing
            return self.process_results_subtask()
        else:
            raise Exception('No subtasks remaining')

    def process_lb_subtask(self):
        #Prepare the necessary files to run the load balancing task on condor

        filenames = self.copasi_model.prepare_ps_load_balancing()
        #Construct the model files for this task
        timeout = str(settings.IDEAL_JOB_TIME * 60)
        if self.task.get_custom_field('rank'):
            rank = str(self.task.get_custom_field('rank'))
        else:
            rank = ''

        #model_filename = self.task.original_model

        copasi_binary_dir, copasi_binary = os.path.split(
            settings.COPASI_LOCAL_BINARY)

        #write the load balancing script
        load_balacing_script_template = Template(
            load_balancing.load_balancing_string)
        load_balancing_script_string = load_balacing_script_template.substitute(
            timeout=timeout,
            copasi_binary='./' + copasi_binary,
            copasi_file_1=('load_balancing_1.cps'),
            copasi_file_10=('load_balancing_10.cps'),
            copasi_file_100=('load_balancing_100.cps'),
            copasi_file_1000=('load_balancing_1000.cps'),
        )
        load_balancing_script_filename = 'load_balance.sh'
        load_balancing_file = open(
            os.path.join(self.task.directory, load_balancing_script_filename),
            'w')
        load_balancing_file.write(load_balancing_script_string)
        load_balancing_file.close()

        copasi_files_string = ''
        for repeat in [1, 10, 100, 1000]:
            copasi_files_string += 'load_balancing_%d.cps, ' % repeat
        copasi_files_string = copasi_files_string.rstrip(
            ', ')  #Remove final comma

        load_balancing_condor_template = Template(
            condor_spec.condor_string_header +
            condor_spec.load_balancing_spec_string)
        load_balancing_condor_string = load_balancing_condor_template.substitute(
            pool_type=self.task.condor_pool.pool_type,
            pool_address=self.task.condor_pool.address,
            script=load_balancing_script_filename,
            copasi_binary=settings.COPASI_LOCAL_BINARY,
            arguments=str(timeout),
            rank=rank,
            copasi_files=copasi_files_string,
        )
        #write to the condor file
        condor_file = open(
            os.path.join(self.task.directory, 'load_balancing.job'), 'w')
        condor_file.write(load_balancing_condor_string)
        condor_file.close()

        subtask = self.get_subtask(1)

        subtask.spec_file = 'load_balancing.job'
        subtask.status = 'waiting'

        subtask.set_custom_field('std_output_file', 'load_balancing.out')
        subtask.set_custom_field('std_err_file', 'load_balancing.err')
        subtask.set_custom_field('log_file', 'load_balancing.log')
        subtask.set_custom_field('job_output', '')
        subtask.set_custom_field('copasi_model', 'load_balancing.cps')

        subtask.save()

        return subtask

    def process_main_subtask(self):

        #Get the correct subtask
        if self.use_load_balancing:
            subtask = self.get_subtask(2)

            lb_job = CondorJob.objects.get(subtask=self.get_subtask(1))
            #Read the load_balancing.out file

            output = open(
                os.path.join(subtask.task.directory, lb_job.std_output_file),
                'r')

            for line in output.readlines():
                line = line.rstrip('\n')
                if line != '':
                    repeats_str, time_str = line.split(' ')

                try:
                    lb_repeats = int(repeats_str)
                    time = float(time_str)
                except Exception, e:
                    log.exception(e)
                    lb_repeats = 1
                    time = settings.IDEAL_JOB_TIME

                time_per_step = time / lb_repeats

        else:
Beispiel #4
0
class TaskPlugin(BaseTask):
    
    subtasks = 3

    def __init__(self, task):
        self.use_load_balancing = not task.get_custom_field('skip_load_balancing_step')

        if self.use_load_balancing:
            self.subtasks = 3
        else:
            self.subtasks = 2
            task.set_custom_field('repeats_per_job', 1)
            task.save()
            
        super(TaskPlugin, self).__init__(task)
        self.copasi_model = PSCopasiModel(os.path.join(self.task.directory, self.task.original_model))

        
    def validate(self):
        #TODO:Abstract this to a new COPASI class in this plugin package
        return self.copasi_model.is_valid('PS')

    def initialize_subtasks(self):
        #Create new subtask objects, and save them
        if self.use_load_balancing:
            #Create the load balancing module
            self.create_new_subtask('lb')
        
        #The main module
        self.create_new_subtask('main')
        #And a subtask to process any results
        self.create_new_subtask('process', local=True)
        
    def prepare_subtask(self, index):
        """Prepare the indexed subtask"""
        
        if index == 1:
            if self.use_load_balancing:
                return self.process_lb_subtask()
            else:
                return self.process_main_subtask()
        
        elif index == 2:
            if self.use_load_balancing:
                return self.process_main_subtask()
            else:
                return self.process_results_subtask()
        elif index == 3:
            assert self.use_load_balancing
            return self.process_results_subtask()
        else:
            raise Exception('No subtasks remaining')


    def process_lb_subtask(self):
        #Prepare the necessary files to run the load balancing task on condor
        
        filenames = self.copasi_model.prepare_ps_load_balancing()
        #Construct the model files for this task
        timeout = str(settings.IDEAL_JOB_TIME * 60)
        if self.task.get_custom_field('rank'):
            rank = str(self.task.get_custom_field('rank'))
        else:
            rank = ''
            
        #model_filename = self.task.original_model
        
        copasi_binary_dir, copasi_binary = os.path.split(settings.COPASI_LOCAL_BINARY)
        
        #write the load balancing script
        load_balacing_script_template = Template(load_balancing.load_balancing_string)
        load_balancing_script_string = load_balacing_script_template.substitute(timeout=timeout,
                                                                 copasi_binary='./' + copasi_binary,
                                                                 copasi_file_1 = ('load_balancing_1.cps'),
                                                                 copasi_file_10 = ('load_balancing_10.cps'),
                                                                 copasi_file_100 = ('load_balancing_100.cps'),
                                                                 copasi_file_1000 = ('load_balancing_1000.cps'),

                                                                 )
        load_balancing_script_filename = 'load_balance.sh'
        load_balancing_file = open(os.path.join(self.task.directory, load_balancing_script_filename), 'w')
        load_balancing_file.write(load_balancing_script_string)
        load_balancing_file.close()
        
        copasi_files_string = ''
        for repeat in [1, 10, 100, 1000]:
            copasi_files_string += 'load_balancing_%d.cps, ' % repeat
        copasi_files_string = copasi_files_string.rstrip(', ') #Remove final comma
        
        load_balancing_condor_template = Template(condor_spec.condor_string_header + condor_spec.load_balancing_spec_string)
        load_balancing_condor_string = load_balancing_condor_template.substitute(pool_type=self.task.condor_pool.pool_type,
                                                                   pool_address = self.task.condor_pool.address,
                                                                   script = load_balancing_script_filename,
                                                                   copasi_binary=settings.COPASI_LOCAL_BINARY,
                                                                   arguments = str(timeout),
                                                                   rank=rank,
                                                                   copasi_files=copasi_files_string,
                                                                   )
        #write to the condor file
        condor_file = open(os.path.join(self.task.directory, 'load_balancing.job'), 'w')
        condor_file.write(load_balancing_condor_string)
        condor_file.close()
        
        subtask=self.get_subtask(1)
        
        subtask.spec_file = 'load_balancing.job'
        subtask.status = 'waiting'
        
        subtask.set_custom_field('std_output_file', 'load_balancing.out')
        subtask.set_custom_field('std_err_file', 'load_balancing.err')
        subtask.set_custom_field('log_file', 'load_balancing.log')
        subtask.set_custom_field('job_output', '')
        subtask.set_custom_field('copasi_model', 'load_balancing.cps')

        
        subtask.save()
        
        return subtask
        
    def process_main_subtask(self):
        

        #Get the correct subtask
        if self.use_load_balancing:
            subtask = self.get_subtask(2)
            
            lb_job = CondorJob.objects.get(subtask=self.get_subtask(1))
            #Read the load_balancing.out file
            
            output = open(os.path.join(subtask.task.directory, lb_job.std_output_file), 'r')
            
            
            for line in output.readlines():
                line = line.rstrip('\n')
                if line != '':
                    repeats_str, time_str = line.split(' ')
                
                try:
                    lb_repeats = int(repeats_str)
                    time = float(time_str)
                except Exception as e:
                    log.exception(e)
                    lb_repeats = 1
                    time = settings.IDEAL_JOB_TIME
                
                time_per_step = time / lb_repeats
                

        else:
            subtask = self.get_subtask(1)
            time_per_step = None
        
        
        
        #If no load balancing step required:
        model_files = self.copasi_model.prepare_ps_jobs(subtask.index, time_per_step)
        
        condor_pool = self.task.condor_pool
        
        condor_job_file = self.copasi_model.prepare_ss_condor_job(condor_pool.pool_type, condor_pool.address, len(model_files), subtask.index, rank='')
        
        log.debug('Prepared copasi files %s'%model_files)
        log.debug('Prepared condor job %s' %condor_job_file)
        
        model_count = len(model_files)
        self.task.set_custom_field('model_count', model_count)
        
        
        subtask.spec_file = condor_job_file
        subtask.status = 'ready'
        subtask.save()
        
        return subtask
        
        
    def process_results_subtask(self):
        subtask=self.get_subtask(2)
        assert isinstance(subtask, Subtask)
        
        subtask.start_time = now()
        
        #Go through and collate the results
        #This is reasonably computationally simple, so we run locally
                
        directory = self.task.directory        
        
        
        if self.use_load_balancing:
            main_subtask = self.get_subtask(2)
            subtask = self.get_subtask(3)
        else:
            main_subtask = self.get_subtask(1)
            subtask = self.get_subtask(2)
        
        main_jobs = CondorJob.objects.filter(subtask=main_subtask)
        
        results_files = [job.job_output for job in main_jobs]
        
        self.copasi_model.process_ps_results(results_files)
                
        subtask.status = 'finished'
        subtask.finish_time = now()
        subtask.set_run_time(time_delta=subtask.finish_time - subtask.start_time)
        subtask.save()
        
        self.task.results_view=False
        self.task.save()
        
        return subtask
    
    
    
    #===========================================================================
    # Results download code. No results view page for this task
    #===========================================================================
    
    
        
    def get_results_download_data(self, request):
        page_name = request.GET.get('name', 'main')
        
        if page_name == 'main':
            #Return the file results.txt
            filename = os.path.join(self.task.directory, 'results.txt')
            if not os.path.isfile(filename):
                request.session['errors'] = [('Cannot Return Output', 'There was an internal error processing the results file')]
                return HttpResponseRedirect(reverse_lazy('task_details', kwargs={'task_id':self.task.id}))
            result_file = open(filename, 'r')
            response = HttpResponse(result_file, content_type='text/tab-separated-values')
            response['Content-Disposition'] = 'attachment; filename=%s_results.txt' % (self.task.name.replace(' ', '_'))
            response['Content-Length'] = os.path.getsize(filename)
   
            return response
Beispiel #5
0
class TaskPlugin(BaseTask):
    
    subtasks = 3

    def __init__(self, task):
        self.use_load_balancing = not task.get_custom_field('skip_load_balancing_step')

        if self.use_load_balancing:
            self.subtasks = 3
        else:
            self.subtasks = 2
            task.set_custom_field('repeats_per_job', 1)
            task.save()
            
        super(TaskPlugin, self).__init__(task)
        self.copasi_model = PSCopasiModel(os.path.join(self.task.directory, self.task.original_model))

        
    def validate(self):
        #TODO:Abstract this to a new COPASI class in this plugin package
        return self.copasi_model.is_valid('PS')

    def initialize_subtasks(self):
        #Create new subtask objects, and save them
        if self.use_load_balancing:
            #Create the load balancing module
            self.create_new_subtask('lb')
        
        #The main module
        self.create_new_subtask('main')
        #And a subtask to process any results
        self.create_new_subtask('process', local=True)
        
    def prepare_subtask(self, index):
        """Prepare the indexed subtask"""
        
        if index == 1:
            if self.use_load_balancing:
                return self.process_lb_subtask()
            else:
                return self.process_main_subtask()
        
        elif index == 2:
            if self.use_load_balancing:
                return self.process_main_subtask()
            else:
                return self.process_results_subtask()
        elif index == 3:
            assert self.use_load_balancing
            return self.process_results_subtask()
        else:
            raise Exception('No subtasks remaining')


    def process_lb_subtask(self):
        #Prepare the necessary files to run the load balancing task on condor
        
        filenames = self.copasi_model.prepare_ps_load_balancing()
        #Construct the model files for this task
        timeout = str(settings.IDEAL_JOB_TIME * 60)
        if self.task.get_custom_field('rank'):
            rank = str(self.task.get_custom_field('rank'))
        else:
            rank = ''
            
        #model_filename = self.task.original_model
        
        copasi_binary_dir, copasi_binary = os.path.split(settings.COPASI_LOCAL_BINARY)
        
        #write the load balancing script
        load_balacing_script_template = Template(load_balancing.load_balancing_string)
        load_balancing_script_string = load_balacing_script_template.substitute(timeout=timeout,
                                                                 copasi_binary='./' + copasi_binary,
                                                                 copasi_file_1 = ('load_balancing_1.cps'),
                                                                 copasi_file_10 = ('load_balancing_10.cps'),
                                                                 copasi_file_100 = ('load_balancing_100.cps'),
                                                                 copasi_file_1000 = ('load_balancing_1000.cps'),

                                                                 )
        load_balancing_script_filename = 'load_balance.sh'
        load_balancing_file = open(os.path.join(self.task.directory, load_balancing_script_filename), 'w')
        load_balancing_file.write(load_balancing_script_string)
        load_balancing_file.close()
        
        copasi_files_string = ''
        for repeat in [1, 10, 100, 1000]:
            copasi_files_string += 'load_balancing_%d.cps, ' % repeat
        copasi_files_string = copasi_files_string.rstrip(', ') #Remove final comma
        
        load_balancing_condor_template = Template(condor_spec.condor_string_header + condor_spec.load_balancing_spec_string)
        load_balancing_condor_string = load_balancing_condor_template.substitute(pool_type=self.task.condor_pool.pool_type,
                                                                   pool_address = self.task.condor_pool.address,
                                                                   script = load_balancing_script_filename,
                                                                   copasi_binary=settings.COPASI_LOCAL_BINARY,
                                                                   arguments = str(timeout),
                                                                   rank=rank,
                                                                   copasi_files=copasi_files_string,
                                                                   )
        #write to the condor file
        condor_file = open(os.path.join(self.task.directory, 'load_balancing.job'), 'w')
        condor_file.write(load_balancing_condor_string)
        condor_file.close()
        
        subtask=self.get_subtask(1)
        
        subtask.spec_file = 'load_balancing.job'
        subtask.status = 'waiting'
        
        subtask.set_custom_field('std_output_file', 'load_balancing.out')
        subtask.set_custom_field('std_err_file', 'load_balancing.err')
        subtask.set_custom_field('log_file', 'load_balancing.log')
        subtask.set_custom_field('job_output', '')
        subtask.set_custom_field('copasi_model', 'load_balancing.cps')

        
        subtask.save()
        
        return subtask
        
    def process_main_subtask(self):
        

        #Get the correct subtask
        if self.use_load_balancing:
            subtask = self.get_subtask(2)
            
            lb_job = CondorJob.objects.get(subtask=self.get_subtask(1))
            #Read the load_balancing.out file
            
            output = open(os.path.join(subtask.task.directory, lb_job.std_output_file), 'r')
            
            
            for line in output.readlines():
                line = line.rstrip('\n')
                if line != '':
                    repeats_str, time_str = line.split(' ')
                
                try:
                    lb_repeats = int(repeats_str)
                    time = float(time_str)
                except Exception, e:
                    log.exception(e)
                    lb_repeats = 1
                    time = settings.IDEAL_JOB_TIME
                
                time_per_step = time / lb_repeats
                

        else: