def __init__(self, task):
self.use_load_balancing = not task.get_custom_field('skip_load_balancing_step')
self.data_files = task.get_custom_field('data_files')
if self.use_load_balancing:
self.subtasks = 4
else:
self.subtasks = 3
task.set_custom_field('repeats_per_job', 1)
super(TaskPlugin, self).__init__(task)
self.copasi_model = PRCopasiModel(os.path.join(self.task.directory, self.task.original_model))
self.repeats = self.task.get_custom_field('repeats')
self.custom_report = self.task.get_custom_field('custom_report')
repeats = self.repeats
def __init__(self, task):
self.use_load_balancing = not task.get_custom_field("skip_load_balancing_step")
self.data_files = task.get_custom_field("data_files")
if self.use_load_balancing:
self.subtasks = 4
else:
self.subtasks = 3
task.set_custom_field("repeats_per_job", 1)
super(TaskPlugin, self).__init__(task)
self.copasi_model = PRCopasiModel(os.path.join(self.task.directory, self.task.original_model))
self.repeats = self.task.get_custom_field("repeats")
self.custom_report = self.task.get_custom_field("custom_report")
repeats = self.repeats
class TaskPlugin(BaseTask):
subtasks = 2
def __init__(self, task):
self.use_load_balancing = not task.get_custom_field('skip_load_balancing_step')
self.data_files = task.get_custom_field('data_files')
if self.use_load_balancing:
self.subtasks = 4
else:
self.subtasks = 3
task.set_custom_field('repeats_per_job', 1)
super(TaskPlugin, self).__init__(task)
self.copasi_model = PRCopasiModel(os.path.join(self.task.directory, self.task.original_model))
self.repeats = self.task.get_custom_field('repeats')
self.custom_report = self.task.get_custom_field('custom_report')
repeats = self.repeats
def validate(self):
#TODO:Abstract this to a new COPASI class in this plugin package
return self.copasi_model.is_valid('PR')
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)
self.create_new_subtask('file')
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:
if self.use_load_balancing:
return self.process_results_subtask()
else:
return self.create_optimal_file()
elif index == 4:
if not self.use_load_balancing:
raise Exception('No subtasks remaining')
else:
return self.create_optimal_file()
def process_lb_subtask(self):
#Prepare the necessary files to run the load balancing task on condor
filenames = self.copasi_model.prepare_pr_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
for data_file in self.data_files:
copasi_files_string += data_file + ', '
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_run = time / lb_repeats
#Work out the number of repeats per job. If this is more than the original number of repeats specified, then just use the original number
repeats_per_job = min(int(round(settings.IDEAL_JOB_TIME * 60 / time_per_run)), self.repeats)
if repeats_per_job < 1:
repeats_per_job = 1
else:
class TaskPlugin(BaseTask):
subtasks = 2
def __init__(self, task):
self.use_load_balancing = not task.get_custom_field("skip_load_balancing_step")
self.data_files = task.get_custom_field("data_files")
if self.use_load_balancing:
self.subtasks = 4
else:
self.subtasks = 3
task.set_custom_field("repeats_per_job", 1)
super(TaskPlugin, self).__init__(task)
self.copasi_model = PRCopasiModel(os.path.join(self.task.directory, self.task.original_model))
self.repeats = self.task.get_custom_field("repeats")
self.custom_report = self.task.get_custom_field("custom_report")
repeats = self.repeats
def validate(self):
# TODO:Abstract this to a new COPASI class in this plugin package
return self.copasi_model.is_valid("PR")
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)
self.create_new_subtask("file")
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:
if self.use_load_balancing:
return self.process_results_subtask()
else:
return self.create_optimal_file()
elif index == 4:
if not self.use_load_balancing:
raise Exception("No subtasks remaining")
else:
return self.create_optimal_file()
def process_lb_subtask(self):
# Prepare the necessary files to run the load balancing task on condor
filenames = self.copasi_model.prepare_pr_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
for data_file in self.data_files:
copasi_files_string += data_file + ", "
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_run = time / lb_repeats
# Work out the number of repeats per job. If this is more than the original number of repeats specified, then just use the original number
repeats_per_job = min(int(round(settings.IDEAL_JOB_TIME * 60 / time_per_run)), self.repeats)
if repeats_per_job < 1:
repeats_per_job = 1
else: