def soap_run(self, ps, **kw):
response = SimulatorService.soap_run(self, ps, **kw)
request = ps.Parse(runRequest.typecode)
print "received run request"
#extract the epidemic model input object from the request
cfg = request._simulatorConfiguration
#example to get the number of time steps in the simulation
#run_length = cfg._simulatorTimeSpecification._runLength
'''ACME code here'''
response._runId = "1"
return response
def soap_run(self, ps, **kw):
response = SimulatorService.soap_run(self, ps, **kw)
request = ps.Parse(runRequest.typecode)
print "received run request"
#extract the epidemic model input object from the request
cfg = request._simulatorConfiguration
#example to get the number of time steps in the simulation
#run_length = cfg._simulatorTimeSpecification._runLength
'''ACME code here'''
response._runId = "1"
return response
def soap_run(self, ps, **kw):
fredConn._setup()
response = SimulatorService.soap_run(self, ps, **kw)
request = ps.Parse(runRequest.typecode)
#extract the epidemic model input object from the request
print "received run request"
cfg = request._simulatorConfiguration
#get the number of time steps in the simulation
run_length = cfg._simulatorTimeSpecification._runLength
#log the EpidemicModelInput request to a log file
self.utils.log_simulatorConfiguration(cfg)
### STB CREATE FRED INPUT FILE
### do some error checking for this version of the model
if cfg._simulatorTimeSpecification._timeStepUnit.lower() != 'days':
print ('This verison of FRED only supports time_step_unit of days')
print ('Apollo sent %s'%(cfg._simulatorTimeSpecification._timeStepUnit))
#### Put in Error Handling, have to ask John L.
if cfg._simulatorTimeSpecification._timeStepValue != 1:
print ('This version of FRED only supports a time_step_value of 1')
print ('Apollo sent %d'%(cfg._simulatorTimeSpecification._timeStepValue))
#### Put in Error Handling, have to ask John L.
print ('WARNING: This service is currently ignoring infectious_period')
print ('WARNING: This service is currently ignoring latent_period')
### Make a random directory name so that multiple calls can be made
randID = random.randint(0,100000)
tempDirName = "fred.tmp.%d"%(randID)
try:
os.mkdir(tempDirName)
except:
raise RuntimeError("Cannot make temporary FRED directory %s"%(tempDirName))
os.chdir(tempDirName)
doVacc = False
with open('fred_input.params','wb') as f:
f.write('days = %d\n'%cfg._simulatorTimeSpecification._runLength)
f.write('symp[0] = %g\n'%cfg._disease._asymptomaticInfectionFraction)
f.write('R0 = %g\n'%cfg._disease._reproductionNumber)
f.write('primary_cases_file[0] = fred_initial_population_0.txt\n')
f.write('residual_immunity_ages[0] = 2 0 100\n')
totPop = self.utils.getTotalPopCount(cfg)
numImmune = self.utils.getPopCountGivenLocationAndDiseaseState(cfg, "ignoreed", "recovered")
percent_immune = float(numImmune)/float(totPop)
f.write('residual_immunity_values[0] = 1 %g\n'%(percent_immune))
f.write('track_infection_events = 1\n')
if sum(cfg._vaccinationControlMeasure._vaccineSupplySchedule) > 0.0:
doVacc = True
#print ('WARNING: This sevice is currently ignoring vaccine_cm_compliance due to someone f*****g FRED up')
f.write("##### VACCINE PARAMETERS\n")
f.write("enable_behaviors = 1\n")
f.write("enable_vaccination = 1\n")
f.write("number_of_vaccines = 1\n")
f.write("accept_vaccine_enabled = 1\n")
f.write("accept_vaccine_strategy_distribution = 7 %g %g 0 0 0 0 0\n"\
%(1.0-cfg._vaccinationControlMeasure._vaccineCmCompliance,\
cfg._vaccinationControlMeasure._vaccineCmCompliance))
f.write("### VACCINE 1\n")
f.write("vaccine_number_of_doses[0] = 1\n")
# Setting this to infinity for now
# need to implement production as a time map as well
f.write("vaccine_total_avail[0] = 300000000\n")
f.write("vaccine_additional_per_day[0] = 300000000\n")
f.write("vaccine_starting_day[0] = 0\n")
f.write("##### Vaccine 1 Dose 0\n")
f.write("vaccine_next_dosage_day[0][0] = 0\n")
f.write("vaccine_dose_efficacy_ages[0][0] = 2 0 100\n")
f.write("vaccine_dose_efficacy_values[0][0] = 1 %g\n"\
%cfg._vaccinationControlMeasure._vaccineEfficacy)
f.write("vaccine_dose_efficacy_delay_ages[0][0] = 2 0 100\n")
f.write("vaccine_dose_efficacy_delay_values[0][0] = 1 %d\n"\
%cfg._vaccinationControlMeasure._vaccineEfficacyDelay)
f.write("vaccination_capacity_file = fred-vaccination-schedule_0.txt\n")
with open('fred-vaccination-schedule_0.txt','wb') as g:
vaccineSupplySchedule = cfg._vaccinationControlMeasure._vaccineSupplySchedule
vaccineAdminSchedule = cfg._vaccinationControlMeasure._vaccinationAdminSchedule
for day in range(0,len(vaccineSupplySchedule)) :
## Hack for now, because I don't have the resolution on production in FRED
g.write("%d %d\n"%(day,min(vaccineSupplySchedule[day],vaccineAdminSchedule[day])))
with open('fred_initial_population_0.txt','wb') as f:
f.write('#line_format\n')
numInfectious = self.utils.getPopCountGivenLocationAndDiseaseState(cfg, "ignored", "infectious")
#f.write('0 0 %d\n'%(cfg._disease_dynamics._pop_count[2]))
f.write('0 0 %d\n'%(numInfectious))
### if vaccination comes through, parse this
with open('starttime','wb') as f:
f.write('Nothing')
idPrefix = cfg._simulatorIdentification._simulatorDeveloper +\
"_" + cfg._simulatorIdentification._simulatorName +\
"_" + cfg._simulatorIdentification._simulatorVersion + "_"
fredConn._connect()
### Write the PBS submission Script
with open('fred_submit.pbs','wb') as f:
f.write('#!/bin/csh\n')
if fredConn.machine == "blacklight.psc.xsede.org":
f.write('#PBS -l ncpus=16\n')
else:
f.write('#PBS -l nodes=2:ppn=8\n')
f.write('#PBS -N fred.pbs.out\n')
f.write('#PBS -l walltime=30:00\n')
f.write('#PBS -j oe\n')
if fredConn.machine == "blacklight.psc.xsede.org":
f.write('#PBS -q debug\n')
f.write('\n')
if fredConn.machine == "blacklight.psc.xsede.org":
f.write('source /usr/share/modules/init/csh\n')
f.write('source /etc/csh.cshrc.psc\n')
f.write('module load fred\n')
f.write('module load python\n')
f.write('cd $PBS_O_WORKDIR\n')
f.write('echo `date` > starttime\n')
f.write('### Get the PBS ID\n')
f.write("set words = `echo $PBS_JOBID | sed 's/\./ /g'`\n")
f.write("set id = $words[1]\n")
f.write('fred_job -p fred_input.params -n 8 -t 2 -m 8 -k %s$id\n'%idPrefix)
f.write('touch .dbloading\n')
f.write('python $FRED_HOME/bin/fred_to_apollo_parallel.py -k %s$id\n'%(idPrefix))
f.write('rm -rf .dbloading\n')
#f.write('echo COMPLETED > job_status')
### for a direct Job.. write the csh script to run FRED
with open('fred_run.csh','wb') as f:
f.write('#!/bin/csh\n')
f.write('echo `date` > starttime\n')
f.write('### Generate Timestamp for ID\n')
f.write('fred_job -p fred_input.params -n 4 -t 2 -m 4 -k %s$id > out.run\n'%idPrefix)
f.write('touch .dbloading\n')
f.write('python $FRED_HOME/bin/fred_to_apollo_parallel.py -k %s$id >& out.db\n'%idPrefix)
f.write('rm -rf .dbloading\n')
os.chdir('../')
#fredConn._setup("warhol.psc.edu",username="******",privateKeyFile="./id_rsa")
#fredConn._connect()
#print "Created Connection"
fredConn._mkdir(tempDirName)
fredConn._sendFile(tempDirName+'/fred_submit.pbs')
fredConn._sendFile(tempDirName+'/fred_run.csh')
fredConn._sendFile(tempDirName+'/fred_input.params')
fredConn._sendFile(tempDirName+'/fred_initial_population_0.txt')
fredConn._sendFile(tempDirName+'/starttime')
if doVacc:
fredConn._sendFile(tempDirName+"/fred-vaccination-schedule_0.txt")
### we do not need temp directory anymore
shutil.rmtree(tempDirName)
print "Running FRED"
sys.stdout.flush()
#returnVal = fredConn._submitPBSJob(randID)
returnVal = fredConn._submitJob(randID)
print returnVal
### parse the run ID
response._runId = idPrefix + str(returnVal)
#ssh.close()
#sftp.close()
return response
def soap_run(self, ps, **kw):
fredConn._setup()
response = SimulatorService.soap_run(self, ps, **kw)
request = ps.Parse(runRequest.typecode)
#extract the epidemic model input object from the request
print "received run request"
cfg = request._simulatorConfiguration
#get the number of time steps in the simulation
run_length = cfg._simulatorTimeSpecification._runLength
#log the EpidemicModelInput request to a log file
self.utils.log_simulatorConfiguration(cfg)
### STB CREATE FRED INPUT FILE
### do some error checking for this version of the model
if cfg._simulatorTimeSpecification._timeStepUnit.lower() != 'days':
print('This verison of FRED only supports time_step_unit of days')
print('Apollo sent %s' %
(cfg._simulatorTimeSpecification._timeStepUnit))
#### Put in Error Handling, have to ask John L.
if cfg._simulatorTimeSpecification._timeStepValue != 1:
print('This version of FRED only supports a time_step_value of 1')
print('Apollo sent %d' %
(cfg._simulatorTimeSpecification._timeStepValue))
#### Put in Error Handling, have to ask John L.
print('WARNING: This service is currently ignoring infectious_period')
print('WARNING: This service is currently ignoring latent_period')
### Make a random directory name so that multiple calls can be made
randID = random.randint(0, 100000)
tempDirName = "fred.tmp.%d" % (randID)
try:
os.mkdir(tempDirName)
except:
raise RuntimeError("Cannot make temporary FRED directory %s" %
(tempDirName))
os.chdir(tempDirName)
doVacc = False
with open('fred_input.params', 'wb') as f:
f.write('days = %d\n' % cfg._simulatorTimeSpecification._runLength)
f.write('symp[0] = %g\n' %
cfg._disease._asymptomaticInfectionFraction)
f.write('R0 = %g\n' % cfg._disease._reproductionNumber)
f.write('primary_cases_file[0] = fred_initial_population_0.txt\n')
f.write('residual_immunity_ages[0] = 2 0 100\n')
totPop = self.utils.getTotalPopCount(cfg)
numImmune = self.utils.getPopCountGivenLocationAndDiseaseState(
cfg, "ignoreed", "recovered")
percent_immune = float(numImmune) / float(totPop)
f.write('residual_immunity_values[0] = 1 %g\n' % (percent_immune))
f.write('track_infection_events = 1\n')
if sum(cfg._vaccinationControlMeasure._vaccineSupplySchedule
) > 0.0:
doVacc = True
#print ('WARNING: This sevice is currently ignoring vaccine_cm_compliance due to someone f*****g FRED up')
f.write("##### VACCINE PARAMETERS\n")
f.write("enable_behaviors = 1\n")
f.write("enable_vaccination = 1\n")
f.write("number_of_vaccines = 1\n")
f.write("accept_vaccine_enabled = 1\n")
f.write("accept_vaccine_strategy_distribution = 7 %g %g 0 0 0 0 0\n"\
%(1.0-cfg._vaccinationControlMeasure._vaccineCmCompliance,\
cfg._vaccinationControlMeasure._vaccineCmCompliance))
f.write("### VACCINE 1\n")
f.write("vaccine_number_of_doses[0] = 1\n")
# Setting this to infinity for now
# need to implement production as a time map as well
f.write("vaccine_total_avail[0] = 300000000\n")
f.write("vaccine_additional_per_day[0] = 300000000\n")
f.write("vaccine_starting_day[0] = 0\n")
f.write("##### Vaccine 1 Dose 0\n")
f.write("vaccine_next_dosage_day[0][0] = 0\n")
f.write("vaccine_dose_efficacy_ages[0][0] = 2 0 100\n")
f.write("vaccine_dose_efficacy_values[0][0] = 1 %g\n"\
%cfg._vaccinationControlMeasure._vaccineEfficacy)
f.write("vaccine_dose_efficacy_delay_ages[0][0] = 2 0 100\n")
f.write("vaccine_dose_efficacy_delay_values[0][0] = 1 %d\n"\
%cfg._vaccinationControlMeasure._vaccineEfficacyDelay)
f.write(
"vaccination_capacity_file = fred-vaccination-schedule_0.txt\n"
)
with open('fred-vaccination-schedule_0.txt', 'wb') as g:
vaccineSupplySchedule = cfg._vaccinationControlMeasure._vaccineSupplySchedule
vaccineAdminSchedule = cfg._vaccinationControlMeasure._vaccinationAdminSchedule
for day in range(0, len(vaccineSupplySchedule)):
## Hack for now, because I don't have the resolution on production in FRED
g.write("%d %d\n" % (day,
min(vaccineSupplySchedule[day],
vaccineAdminSchedule[day])))
with open('fred_initial_population_0.txt', 'wb') as f:
f.write('#line_format\n')
numInfectious = self.utils.getPopCountGivenLocationAndDiseaseState(
cfg, "ignored", "infectious")
#f.write('0 0 %d\n'%(cfg._disease_dynamics._pop_count[2]))
f.write('0 0 %d\n' % (numInfectious))
### if vaccination comes through, parse this
with open('starttime', 'wb') as f:
f.write('Nothing')
idPrefix = cfg._simulatorIdentification._simulatorDeveloper +\
"_" + cfg._simulatorIdentification._simulatorName +\
"_" + cfg._simulatorIdentification._simulatorVersion + "_"
fredConn._connect()
### Write the PBS submission Script
with open('fred_submit.pbs', 'wb') as f:
f.write('#!/bin/csh\n')
if fredConn.machine == "blacklight.psc.xsede.org":
f.write('#PBS -l ncpus=16\n')
else:
f.write('#PBS -l nodes=2:ppn=8\n')
f.write('#PBS -N fred.pbs.out\n')
f.write('#PBS -l walltime=30:00\n')
f.write('#PBS -j oe\n')
if fredConn.machine == "blacklight.psc.xsede.org":
f.write('#PBS -q debug\n')
f.write('\n')
if fredConn.machine == "blacklight.psc.xsede.org":
f.write('source /usr/share/modules/init/csh\n')
f.write('source /etc/csh.cshrc.psc\n')
f.write('module load fred\n')
f.write('module load python\n')
f.write('cd $PBS_O_WORKDIR\n')
f.write('echo `date` > starttime\n')
f.write('### Get the PBS ID\n')
f.write("set words = `echo $PBS_JOBID | sed 's/\./ /g'`\n")
f.write("set id = $words[1]\n")
f.write('fred_job -p fred_input.params -n 8 -t 2 -m 8 -k %s$id\n' %
idPrefix)
f.write('touch .dbloading\n')
f.write(
'python $FRED_HOME/bin/fred_to_apollo_parallel.py -k %s$id\n' %
(idPrefix))
f.write('rm -rf .dbloading\n')
#f.write('echo COMPLETED > job_status')
### for a direct Job.. write the csh script to run FRED
with open('fred_run.csh', 'wb') as f:
f.write('#!/bin/csh\n')
f.write('echo `date` > starttime\n')
f.write('### Generate Timestamp for ID\n')
f.write(
'fred_job -p fred_input.params -n 4 -t 2 -m 4 -k %s$id > out.run\n'
% idPrefix)
f.write('touch .dbloading\n')
f.write(
'python $FRED_HOME/bin/fred_to_apollo_parallel.py -k %s$id >& out.db\n'
% idPrefix)
f.write('rm -rf .dbloading\n')
os.chdir('../')
#fredConn._setup("warhol.psc.edu",username="******",privateKeyFile="./id_rsa")
#fredConn._connect()
#print "Created Connection"
fredConn._mkdir(tempDirName)
fredConn._sendFile(tempDirName + '/fred_submit.pbs')
fredConn._sendFile(tempDirName + '/fred_run.csh')
fredConn._sendFile(tempDirName + '/fred_input.params')
fredConn._sendFile(tempDirName + '/fred_initial_population_0.txt')
fredConn._sendFile(tempDirName + '/starttime')
if doVacc:
fredConn._sendFile(tempDirName +
"/fred-vaccination-schedule_0.txt")
### we do not need temp directory anymore
shutil.rmtree(tempDirName)
print "Running FRED"
sys.stdout.flush()
#returnVal = fredConn._submitPBSJob(randID)
returnVal = fredConn._submitJob(randID)
print returnVal
### parse the run ID
response._runId = idPrefix + str(returnVal)
#ssh.close()
#sftp.close()
return response
def soap_run(self, ps, **kw):
fredConn._setup()
response = SimulatorService.soap_run(self, ps, **kw)
request = ps.Parse(runRequest.typecode)
#extract the epidemic model input object from the request
print "received run request"
cfg = request._simulatorConfiguration
#log the EpidemicModelInput request to a log file
self.utils.log_simulatorConfiguration(cfg)
### get population file for fractions
fipsCountDict = {}
with open("2005_2009_ver2_pop_counts_by_fips.txt","rb") as f:
for line in f:
fipsCountDict[line.split()[0]] = int(line.split()[1].strip())
### STB CREATE FRED INPUT FILE
### do some error checking for this version of the model
print cfg._simulatorTimeSpecification._timeStepUnit
if cfg._simulatorTimeSpecification._timeStepUnit.lower() != 'day':
print ('This verison of FRED only supports time_step_unit of day')
print ('Apollo sent %s'%(cfg._simulatorTimeSpecification._timeStepUnit))
#### Put in Error Handling, have to ask John L.
response._runId = -401
return response
if cfg._simulatorTimeSpecification._timeStepValue != 1:
print ('This version of FRED only supports a time_step_value of 1')
print ('Apollo sent %d'%(cfg._simulatorTimeSpecification._timeStepValue))
response._runId = -402
return response
lenLoc = len(cfg._populationInitialization._populationLocation)
print "lenLoc = " + str(lenLoc)
if lenLoc != 5 and lenLoc != 2:
print ('This version of the FRED only supports 2 (state) or 5 (county) NSIDS codes')
response._runId = -403
return response
if cfg._populationInitialization._populationLocation not in fipsCountDict.keys():
print ('The location specified does not have a total population')
response._runId = -406
return response
### Make a random directory name so that multiple calls can be made
randID = random.randint(0,100000)
tempDirName = "fred.tmp.%d"%(randID)
try:
os.mkdir(tempDirName)
except:
print("Cannot make temporary FRED directory %s"%(tempDirName))
response._runId = -404
return response
fredInput = FredInputFileSet(cfg,tempDirName,fipsCountDict,self)
fredInput.createParam()
fredInput.parseControlMeasures()
os.chdir(tempDirName)
with open('starttime','wb') as f:
f.write('Nothing')
idPrefix = cfg._simulatorIdentification._softwareDeveloper +\
"_" + cfg._simulatorIdentification._softwareName +\
"_" + cfg._simulatorIdentification._softwareVersion + "_"
fredConn.writeRunScript(idPrefix)
os.chdir('../')
fredConn._setup()
fredConn._connect()
fredConn._mkdir(tempDirName)
for fileNames in fredInput.fileList:
fredConn._sendFile(tempDirName+'/'+fileNames)
fredConn._sendFile(tempDirName+ '/' + fredConn.runScriptName)
fredConn._sendFile(tempDirName+'/starttime')
### we do not need temp directory anymore
shutil.rmtree(tempDirName)
print "Running FRED"
sys.stdout.flush()
#returnVal = fredConn._submitPBSJob(randID)
returnVal = fredConn._submitJob(randID)
print returnVal
### parse the run ID
response._runId = idPrefix + str(returnVal)
#ssh.close()
#sftp.close()
return response