def update_tasks(user=None, task=None):
"""Examines the status of all CondorJob objects. If the status of upstream subtasks and tasks need changing, then this is done.
If requested, can filter by a specific user or subtask
"""
#Step 1: Get a list of running tasks
#log.debug('Checking running tasks')
tasks = Task.objects.filter(status='running')
if user:
tasks = tasks.filter(user = user)
if task:
tasks = tasks.filter(id=task.id)
for task in tasks:
#Next, get the corresponding running subtasks
subtasks = Subtask.objects.filter(task=task).filter(status='running')
log.debug(subtasks)
for subtask in subtasks:
#log.debug('Checking subtask status: %s'%subtask.status)
jobs = CondorJob.objects.filter(subtask=subtask)
#Does any of the jobs have an error status? Then mark the whole task as having failed
errors = jobs.filter(status='E') | jobs.filter(status='H')
if errors.count() > 0:
for job in errors:
log.debug('Job %d.%d has status %s. Marking task as errored' % (job.subtask.cluster_id, job.process_id, job.status))
subtask.status = 'error'
task.status = 'error'
subtask.finish_time = now()
subtask.save()
task.save()
break
#TODO: Can we have a more graceful error handling procedure here?
#Next, check to see if all the jobs have finished
finished = jobs.filter(status='F')
if finished.count() == jobs.count():
#The subtask has finished!
log.debug('Task %s, subtask %d: successfully finished. Updating status' % (task.name, subtask.index))
subtask.status = 'finished'
subtask.set_run_time() #Set the run time as the sum from the associated jobs
subtask.set_job_count() #And the number of condor jobs
subtask.finish_time = now()
subtask.save()
else:
#Something not right. TODO: determine if bad exit status, files not transferred yet, etc., and respond appropriatley
#log.debug('%d jobs still in queue.' % (jobs.count() - finished.count()))
pass
#Now go through the subtasks and submit any that are waiting, provided that their preceding one has finished
subtasks = Subtask.objects.filter(task=task).filter(status='waiting').order_by('index')
for subtask in subtasks:
try:
if subtask.index > 1:
previous_subtasks = Subtask.objects.filter(task=task, index=(subtask.index -1))
all_previous_subtasks_finished = True
for previous_subtask in previous_subtasks:
if previous_subtask.status != 'finished': all_previous_subtasks_finished = False
if all_previous_subtasks_finished:
#We have a new subtask to submit
TaskClass = tools.get_task_class(task.task_type)
task_instance = TaskClass(task)
log.debug('Preparing new subtask %d' % (subtask.index))
prepared_subtask = task_instance.prepare_subtask(subtask.index)
#If this wasn't a local subtask, submit to condor
if not subtask.local:
condor_tools.submit_task(prepared_subtask)
except Exception, e:
subtask.status = 'error'
subtask.set_job_count()
subtask.set_run_time()
subtask.finish_time= now()
subtask.save()
task.status = 'error'
task.set_job_count()
task.set_run_time()
task.set_custom_field('error', str(e))
task.finish_time = now()
task.save()
email_tools.send_task_completion_email(task)
#Get the list of subtasks again
task_subtasks = Subtask.objects.filter(task=task)
finished = task_subtasks.filter(status='finished').order_by('index')
if task_subtasks.count() == finished.count():
task.status = 'finished'
task.finish_time = now()
log.debug('Task %s (user %s), all subtasks finished. Marking task as finished.' % (task.name, task.user.username))
task.set_run_time()
task.set_job_count()
#task.trim_condor_jobs() Don't do this, it breaks plugin functionality
task.save()
email_tools.send_task_completion_email(task)
task.last_update_time=now()
task.save()
def post(self, request, *args, **kwargs):
assert isinstance(request, HttpRequest)
assert request.META['CONTENT_TYPE'] == 'application/json'
json_data = request.body
data = json.loads(json_data)
pool_id = data['pool_id']
secret_key = data['secret_key']
pool = EC2Pool.objects.get(uuid=pool_id)
assert pool.secret_key == secret_key
#Get the condor jobs associated with the condor pool which we think are still running
pool_jobs = CondorJob.objects.filter(subtask__task__condor_pool=pool)
running_jobs = pool_jobs.filter(queue_status='R')
idle_jobs = pool_jobs.filter(queue_status='I')
held_jobs = pool_jobs.filter(queue_status='H')
queued_jobs = running_jobs | idle_jobs | held_jobs
for condor_queue_id, queue_status in data['condor_jobs']:
condor_job = queued_jobs.get(queue_id=condor_queue_id)
condor_job.queue_status = queue_status
condor_job.save()
#Since this job appeared in the list, it's not finished
queued_jobs = queued_jobs.exclude(id=condor_job.id)
#Assume that everything left in queued_jobs has finished
for job in queued_jobs:
job.queue_status = 'F'
job.save()
#Get all subtasks that are running on the pool
active_subtasks = Subtask.objects.filter(
task__condor_pool=pool).filter(active=True)
for subtask in active_subtasks:
#Look at all the jobs. Are they all finished?
all_jobs_finished = True
errors = False
for job in subtask.condorjob_set.all():
if job.queue_status != 'F':
all_jobs_finished = False
elif job.queue_status == 'H':
errors = True
if errors:
print(sys.stderr, 'Error!')
subtask.active = False
subtask.status = 'error'
subtask.save()
subtask.task.status = 'error'
subtask.task.save()
elif all_jobs_finished:
print >> sys.stderr, 'All jobs finished'
subtask.active = False
subtask.status = 'finished'
subtask.save()
#Is there another subtask to run?
TaskClass = tools.get_task_class(subtask.task.task_type)
subtask_count = TaskClass.subtasks
task_instance = TaskClass(subtask.task)
if subtask.index < subtask_count:
#We have another subtask to run
print('Another subtask to run!')
task_instance.submit_subtask(subtask.index + 1)
else:
#The task must have finished
#Request the transfer of files
task_instance.request_file_transfer(
subtask.index, 'finished')
#Finally, add instance alarms to the task if needed:
try:
ec2_tools.add_instances_alarms(pool)
except Exception as e:
log.exception(e)
#Construct a json response to send back
response_data = {'status': 'created'}
json_response = json.dumps(response_data)
return HttpResponse(json_response,
content_type="application/json",
status=201)
def form_valid(self, form, *args, **kwargs):
#Check we are authorized to run on this pool
compute_pool = form.cleaned_data['compute_pool']
request = self.request
assert isinstance(compute_pool, CondorPool)
assert compute_pool.user == request.user
log.debug('Submitting task to compute pool %s (%s)' %
(compute_pool.name, compute_pool.get_pool_type()))
########################################################################
#Process the uploaded copasi file (and other files?)
########################################################################
#Handle uploaded files...
#Ensure the directory we're adding the file to exists
if not os.path.exists(settings.STORAGE_DIR):
os.mkdir(settings.STORAGE_DIR)
#And the directory for the user
#Takes the form userid.username
user_dir = '%d.%s' % (request.user.id, request.user.username)
user_dir_path = os.path.join(settings.STORAGE_DIR, user_dir)
if not os.path.exists(user_dir_path):
os.mkdir(user_dir_path)
task = Task()
task.name = form.cleaned_data['name']
task.condor_pool = form.cleaned_data['compute_pool']
task.user = request.user
task.task_type = form.cleaned_data['task_type']
task.original_model = 'original_model.cps'
#Get a list of all fields that are only in the task form, and not in the base
extra_fields = []
base_form = base.BaseTaskForm
for field_name in form.fields:
if field_name not in base_form.base_fields:
extra_fields.append((field_name, form.fields[field_name]))
#We have not yet created the directory to hold the files
directory_created = False
task.save() # Save the task so we can get a valid id
#Save the custom task fields
for field_name, field_object in extra_fields:
#TODO: Is the file a zip file? Try unzipping it...
if isinstance(field_object, forms.FileField) and isinstance(
form.cleaned_data[field_name], UploadedFile):
try:
#Create a directory to store the files for the task
#This will just be the id of the task
task_dir = str(task.id)
task_dir_path = os.path.join(user_dir_path, task_dir)
if os.path.exists(task_dir_path):
os.rename(
task_dir_path,
task_dir_path + '.old.' + str(datetime.now()))
os.mkdir(task_dir_path)
directory_created = True
data_file = request.FILES[field_name]
filename = data_file.name
data_destination = os.path.join(task_dir_path, filename)
form_tools.handle_uploaded_file(data_file,
data_destination)
#Next, attempt to extract the file
#If this fails, assume the file is an ASCII data file, not a zip file
try:
data_files_list = []
z = zipfile.ZipFile(data_destination)
#Record the name of each file in the zipfile
for name in z.namelist():
data_files_list.append(name)
z.extractall(task_dir_path)
except zipfile.BadZipfile:
data_files_list = []
#Assume instead that, if not a zip file, the file must be a data file, so leave it be.
#Write the name of the data file to data_files_list
data_files_list.append(filename)
task.set_custom_field('data_files', data_files_list)
except Exception as e:
log.exception(e)
error_messages = [
'An error occured while preparing the task data files',
str(e),
]
form._errors[NON_FIELD_ERRORS] = forms.forms.ErrorList(
error_messages)
try:
shutil.rmtree(task.directory)
except:
pass
try:
task.delete()
except:
pass
kwargs['form'] = form
return self.form_invalid(self, *args, **kwargs)
else:
task.set_custom_field(field_name,
form.cleaned_data[field_name])
task.save()
try:
if not directory_created:
#Create a directory to store the files for the task
#This will just be the id of the task
task_dir = str(task.id)
task_dir_path = os.path.join(user_dir_path, task_dir)
if os.path.exists(task_dir_path):
os.rename(task_dir_path,
task_dir_path + '.old.' + str(datetime.now()))
os.mkdir(task_dir_path)
task.directory = task_dir_path
task.save()
#Next we need to create the directory to store the files for the task
#working_dir = tempfile.mkdtemp(dir=settings.STORAGE_DIR)
model_file = request.FILES['model_file']
full_filename = os.path.join(task_dir_path, task.original_model)
form_tools.handle_uploaded_file(model_file, full_filename)
TaskClass = tools.get_task_class(form.cleaned_data['task_type'])
task_instance = TaskClass(task)
except Exception as e:
log.exception(e)
error_messages = [
'An error occured while preparing the task model file',
str(e),
]
form._errors[NON_FIELD_ERRORS] = forms.forms.ErrorList(
error_messages)
try:
shutil.rmtree(task.directory)
except:
pass
try:
task.delete()
except:
pass
kwargs['form'] = form
return self.form_invalid(self, *args, **kwargs)
#Validate the task
valid = task_instance.validate()
if valid != True:
#valid message contained in valid hopefully.
error_messages = [
'Model file is not valid for the current task type',
str(valid),
]
form._errors[NON_FIELD_ERRORS] = forms.forms.ErrorList(
error_messages)
shutil.rmtree(task.directory)
task.delete()
kwargs['form'] = form
return self.form_invalid(self, *args, **kwargs)
try:
task_instance.initialize_subtasks()
subtask = task_instance.prepare_subtask(1)
condor_tools.submit_task(subtask)
task.status = 'running'
task.save()
except Exception as e:
log.exception(e)
error_messages = [
'An error occured while preparing the subtask',
str(e),
]
form._errors[NON_FIELD_ERRORS] = forms.forms.ErrorList(
error_messages)
try:
shutil.rmtree(task.directory)
except:
pass
try:
task.delete()
except:
pass
kwargs['form'] = form
return self.form_invalid(self, *args, **kwargs)
return HttpResponseRedirect(
reverse_lazy('task_details', kwargs={'task_id': task.id}))
def update_tasks(user=None, task=None):
"""Examines the status of all CondorJob objects. If the status of upstream subtasks and tasks need changing, then this is done.
If requested, can filter by a specific user or subtask
"""
#Step 1: Get a list of running tasks
#log.debug('Checking running tasks')
tasks = Task.objects.filter(status='running')
if user:
tasks = tasks.filter(user=user)
if task:
tasks = tasks.filter(id=task.id)
for task in tasks:
#Next, get the corresponding running subtasks
subtasks = Subtask.objects.filter(task=task).filter(status='running')
log.debug(subtasks)
for subtask in subtasks:
#log.debug('Checking subtask status: %s'%subtask.status)
jobs = CondorJob.objects.filter(subtask=subtask)
#Does any of the jobs have an error status? Then mark the whole task as having failed
errors = jobs.filter(status='E') | jobs.filter(status='H')
if errors.count() > 0:
for job in errors:
log.debug(
'Job %d.%d has status %s. Marking task as errored' %
(job.subtask.cluster_id, job.process_id, job.status))
subtask.status = 'error'
task.status = 'error'
subtask.finish_time = now()
subtask.save()
task.save()
break
#TODO: Can we have a more graceful error handling procedure here?
#Next, check to see if all the jobs have finished
finished = jobs.filter(status='F')
if finished.count() == jobs.count():
#The subtask has finished!
log.debug(
'Task %s, subtask %d: successfully finished. Updating status'
% (task.name, subtask.index))
subtask.status = 'finished'
subtask.set_run_time(
) #Set the run time as the sum from the associated jobs
subtask.set_job_count() #And the number of condor jobs
subtask.finish_time = now()
subtask.save()
else:
#Something not right. TODO: determine if bad exit status, files not transferred yet, etc., and respond appropriatley
#log.debug('%d jobs still in queue.' % (jobs.count() - finished.count()))
pass
#Now go through the subtasks and submit any that are waiting, provided that their preceding one has finished
subtasks = Subtask.objects.filter(task=task).filter(
status='waiting').order_by('index')
for subtask in subtasks:
try:
if subtask.index > 1:
previous_subtasks = Subtask.objects.filter(
task=task, index=(subtask.index - 1))
all_previous_subtasks_finished = True
for previous_subtask in previous_subtasks:
if previous_subtask.status != 'finished':
all_previous_subtasks_finished = False
if all_previous_subtasks_finished:
#We have a new subtask to submit
TaskClass = tools.get_task_class(task.task_type)
task_instance = TaskClass(task)
log.debug('Preparing new subtask %d' % (subtask.index))
prepared_subtask = task_instance.prepare_subtask(
subtask.index)
#If this wasn't a local subtask, submit to condor
if not subtask.local:
condor_tools.submit_task(prepared_subtask)
except Exception as e:
subtask.status = 'error'
subtask.set_job_count()
subtask.set_run_time()
subtask.finish_time = now()
subtask.save()
task.status = 'error'
task.set_job_count()
task.set_run_time()
task.set_custom_field('error', str(e))
task.finish_time = now()
task.save()
email_tools.send_task_completion_email(task)
#Get the list of subtasks again
task_subtasks = Subtask.objects.filter(task=task)
finished = task_subtasks.filter(status='finished').order_by('index')
if task_subtasks.count() == finished.count():
task.status = 'finished'
task.finish_time = now()
log.debug(
'Task %s (user %s), all subtasks finished. Marking task as finished.'
% (task.name, task.user.username))
task.set_run_time()
task.set_job_count()
#task.trim_condor_jobs() Don't do this, it breaks plugin functionality
task.save()
email_tools.send_task_completion_email(task)
task.last_update_time = now()
task.save()
def post(self, request, *args, **kwargs):
assert isinstance(request, HttpRequest)
assert request.META['CONTENT_TYPE'] == 'application/json'
json_data=request.body
data = json.loads(json_data)
pool_id = data['pool_id']
secret_key = data['secret_key']
pool=EC2Pool.objects.get(uuid=pool_id)
assert pool.secret_key == secret_key
#Get the condor jobs associated with the condor pool which we think are still running
pool_jobs = CondorJob.objects.filter(subtask__task__condor_pool=pool)
running_jobs = pool_jobs.filter(queue_status='R')
idle_jobs = pool_jobs.filter(queue_status='I')
held_jobs = pool_jobs.filter(queue_status='H')
queued_jobs = running_jobs | idle_jobs | held_jobs
for condor_queue_id, queue_status in data['condor_jobs']:
condor_job = queued_jobs.get(queue_id=condor_queue_id)
condor_job.queue_status=queue_status
condor_job.save()
#Since this job appeared in the list, it's not finished
queued_jobs = queued_jobs.exclude(id=condor_job.id)
#Assume that everything left in queued_jobs has finished
for job in queued_jobs:
job.queue_status = 'F'
job.save()
#Get all subtasks that are running on the pool
active_subtasks = Subtask.objects.filter(task__condor_pool=pool).filter(active=True)
for subtask in active_subtasks:
#Look at all the jobs. Are they all finished?
all_jobs_finished = True
errors = False
for job in subtask.condorjob_set.all():
if job.queue_status != 'F':
all_jobs_finished = False
elif job.queue_status == 'H':
errors = True
if errors:
print sys.stderr, 'Error!'
subtask.active=False
subtask.status='error'
subtask.save()
subtask.task.status='error'
subtask.task.save()
elif all_jobs_finished:
print >>sys.stderr, 'All jobs finished'
subtask.active = False
subtask.status = 'finished'
subtask.save()
#Is there another subtask to run?
TaskClass = tools.get_task_class(subtask.task.task_type)
subtask_count = TaskClass.subtasks
task_instance = TaskClass(subtask.task)
if subtask.index < subtask_count:
#We have another subtask to run
print 'Another subtask to run!'
task_instance.submit_subtask(subtask.index + 1)
else:
#The task must have finished
#Request the transfer of files
task_instance.request_file_transfer(subtask.index, 'finished')
#Finally, add instance alarms to the task if needed:
try:
ec2_tools.add_instances_alarms(pool)
except Exception, e:
log.exception(e)