def prepare_data(jobs):
output = ""
for job, variation in jobs:
model = CopasiModel(job.get_filename())
results = model.get_so_results()
for result in results:
output += "['" + result['name'] + "_max'," + str(variation) + "," + result['max_result'] + "],\n"
output += "['" + result['name'] + "_min'," + str(variation) + "," + result['min_result'] + "],\n"
return output
def prepare_data(jobs):
output = ""
for job, variation in jobs:
model = CopasiModel(job.get_filename())
results = model.get_so_results()
for result in results:
output += "['" + result['name'] + "_max'," + str(
variation) + "," + result['max_result'] + "],\n"
output += "['" + result['name'] + "_min'," + str(
variation) + "," + result['min_result'] + "],\n"
return output
def run():
#Set up logging, with the appropriate log level
logging.basicConfig(filename=settings.LOG_FILE,level=settings.LOG_LEVEL, format='%(asctime)s::%(levelname)s::%(message)s', datefmt='%Y-%m-%d, %H:%M:%S')
#Step one, load the jobs that have been confirmed, and need submitting to condor :
new_jobs = models.Job.objects.filter(status='N')
for job in new_jobs:
logging.debug('New job found: ' + str(job.id) + ', user: '******'s been set, use it. Otherwise set to 0
if job.rank != None or job.rank != '':
rank = job.rank
else:
rank = '0'
if job.job_type == 'SO':
condor_jobs = model.prepare_so_condor_jobs(rank=rank)
elif job.job_type == 'SS':
no_of_jobs = model.prepare_ss_task(job.runs, skip_load_balancing=job.skip_load_balancing)
condor_jobs = model.prepare_ss_condor_jobs(no_of_jobs, rank=rank)
elif job.job_type == 'PS':
no_of_jobs = model.prepare_ps_jobs(skip_load_balancing=job.skip_load_balancing)
condor_jobs = model.prepare_ps_condor_jobs(no_of_jobs, rank=rank)
elif job.job_type == 'OR':
no_of_jobs = model.prepare_or_jobs(job.runs, skip_load_balancing=job.skip_load_balancing)
condor_jobs = model.prepare_or_condor_jobs(no_of_jobs, rank=rank)
elif job.job_type == 'PR':
no_of_jobs = model.prepare_pr_jobs(job.runs, skip_load_balancing=job.skip_load_balancing, custom_report=job.custom_report)
condor_jobs = model.prepare_pr_condor_jobs(no_of_jobs, rank=rank)
elif job.job_type == 'SP':
##ALTER
no_of_jobs = model.prepare_sp_jobs(job.runs, skip_load_balancing = job.skip_load_balancing, custom_report=False)
condor_jobs = model.prepare_sp_condor_jobs(no_of_jobs, rank=rank)
elif job.job_type == 'OD':
#No need to prepare the job. This was done as the job was submitted
condor_jobs = model.prepare_od_condor_jobs(rank=rank)
elif job.job_type == 'RW':
no_of_jobs = model.prepare_rw_jobs(job.runs)
condor_jobs = model.prepare_rw_condor_jobs(no_of_jobs, job.raw_mode_args, rank=rank)
else:
continue
for cj in condor_jobs:
try:
condor_job_id = condor_submit(cj['spec_file'], username=str(job.user.username))
#Check that the condor job was submitted successfully
assert condor_job_id != -1
condor_job = models.CondorJob(parent=job, spec_file=cj['spec_file'], std_output_file=cj['std_output_file'], std_error_file = cj['std_error_file'], log_file=cj['log_file'], job_output=cj['job_output'], queue_status='Q', queue_id=condor_job_id)
condor_job.save()
if job.condor_jobs == None:
job.condor_jobs = 1
else:
job.condor_jobs += 1
except:
logging.exception('Error submitting job(s) to Condor; ensure condor scheduler service is running. Job: ' + str(job.id) + ', User: '******'Submitted ' + str(len(condor_jobs)) + ' to Condor')
job.status = 'S'
job.last_update=datetime.datetime.today()
job.save()
except Exception, e:
logging.warning('Error preparing job for condor submission. Job: ' + str(job.id) + ', User: '******'Exception: ' + str(e))
job.status = 'E'
job.last_update=datetime.datetime.today()
job.finish_time=datetime.datetime.today()
try:
zip_up_dir(job)
except:
logging.exception('Exception: could not zip up job directory for job ' + str(job.id))
job.save()
try:
email_notify.send_email(job)
except:
logging.exception('Exception: error sending email')
logging.warning('Error preparing job for condor submission. Job: ' + str(job.id) + ', User: '******'Exception: ' + str(e))
try:
zip_up_dir(job)
except:
logging.exception('Exception: could not zip up job directory for job ' + str(job.id))
############
#Collate the results
#Get the list of jobs marked as finished, waiting for processing
waiting = models.Job.objects.filter(status='W')
for job in waiting:
logging.debug('Processing results for complete job ' + str(job.id) + ', User: '******'SO':
#TODO: doesn't do validation step yet. This step should probably be condorised.
#Mark the job as complete
job.status='C'
job.finish_time=datetime.datetime.today()
job.last_update=datetime.datetime.today()
model.get_so_results(save=True)
try:
zip_up_dir(job)
except:
logging.exception('Exception: could not zip up job directory for job ' + str(job.id))
job.save()
try:
email_notify.send_email(job)
def run():
#Set up logging, with the appropriate log level
logging.basicConfig(filename=settings.LOG_FILE,
level=settings.LOG_LEVEL,
format='%(asctime)s::%(levelname)s::%(message)s',
datefmt='%Y-%m-%d, %H:%M:%S')
#Step one, load the jobs that have been confirmed, and need submitting to condor :
new_jobs = models.Job.objects.filter(status='N')
for job in new_jobs:
logging.debug('New job found: ' + str(job.id) + ', user: '******'s been set, use it. Otherwise set to 0
if job.rank != None or job.rank != '':
rank = job.rank
else:
rank = '0'
if job.job_type == 'SO':
condor_jobs = model.prepare_so_condor_jobs(rank=rank)
elif job.job_type == 'SS':
no_of_jobs = model.prepare_ss_task(
job.runs, skip_load_balancing=job.skip_load_balancing)
condor_jobs = model.prepare_ss_condor_jobs(no_of_jobs,
rank=rank)
elif job.job_type == 'PS':
no_of_jobs = model.prepare_ps_jobs(
skip_load_balancing=job.skip_load_balancing)
condor_jobs = model.prepare_ps_condor_jobs(no_of_jobs,
rank=rank)
elif job.job_type == 'OR':
no_of_jobs = model.prepare_or_jobs(
job.runs, skip_load_balancing=job.skip_load_balancing)
condor_jobs = model.prepare_or_condor_jobs(no_of_jobs,
rank=rank)
elif job.job_type == 'PR':
no_of_jobs = model.prepare_pr_jobs(
job.runs,
skip_load_balancing=job.skip_load_balancing,
custom_report=job.custom_report)
condor_jobs = model.prepare_pr_condor_jobs(no_of_jobs,
rank=rank)
elif job.job_type == 'SP':
##ALTER
no_of_jobs = model.prepare_sp_jobs(
job.runs,
skip_load_balancing=job.skip_load_balancing,
custom_report=False)
condor_jobs = model.prepare_sp_condor_jobs(no_of_jobs,
rank=rank)
elif job.job_type == 'OD':
#No need to prepare the job. This was done as the job was submitted
condor_jobs = model.prepare_od_condor_jobs(rank=rank)
elif job.job_type == 'RW':
no_of_jobs = model.prepare_rw_jobs(job.runs)
condor_jobs = model.prepare_rw_condor_jobs(no_of_jobs,
job.raw_mode_args,
rank=rank)
else:
continue
for cj in condor_jobs:
try:
condor_job_id = condor_submit(cj['spec_file'],
username=str(
job.user.username))
#Check that the condor job was submitted successfully
assert condor_job_id != -1
condor_job = models.CondorJob(
parent=job,
spec_file=cj['spec_file'],
std_output_file=cj['std_output_file'],
std_error_file=cj['std_error_file'],
log_file=cj['log_file'],
job_output=cj['job_output'],
queue_status='Q',
queue_id=condor_job_id)
condor_job.save()
if job.condor_jobs == None:
job.condor_jobs = 1
else:
job.condor_jobs += 1
except:
logging.exception(
'Error submitting job(s) to Condor; ensure condor scheduler service is running. Job: '
+ str(job.id) + ', User: '******'Submitted ' + str(len(condor_jobs)) + ' to Condor')
job.status = 'S'
job.last_update = datetime.datetime.today()
job.save()
except Exception, e:
logging.warning(
'Error preparing job for condor submission. Job: ' +
str(job.id) + ', User: '******'Exception: ' + str(e))
job.status = 'E'
job.last_update = datetime.datetime.today()
job.finish_time = datetime.datetime.today()
try:
zip_up_dir(job)
except:
logging.exception(
'Exception: could not zip up job directory for job ' +
str(job.id))
job.save()
try:
email_notify.send_email(job)
except:
logging.exception('Exception: error sending email')
zip_up_dir(job)
except:
logging.exception(
'Exception: could not zip up job directory for job ' +
str(job.id))
############
#Collate the results
#Get the list of jobs marked as finished, waiting for processing
waiting = models.Job.objects.filter(status='W')
for job in waiting:
logging.debug('Processing results for complete job ' + str(job.id) +
', User: '******'SO':
#TODO: doesn't do validation step yet. This step should probably be condorised.
#Mark the job as complete
job.status = 'C'
job.finish_time = datetime.datetime.today()
job.last_update = datetime.datetime.today()
model.get_so_results(save=True)
try:
zip_up_dir(job)
except:
logging.exception(
'Exception: could not zip up job directory for job ' +
str(job.id))
job.save()