def projectConfig(projectDir):
"""
Return the configuration object representing the project config.
Parameters
----------
projectDir :str
Project directory path as string.
Returns
-------
cp : NepidemiXConfigParser
A configuration object representing the project directory configuration.
"""
# Check so that the directory exists
if not os.path.isdir(projectDir):
raise IOError("Project directory '{0}' does not exist.".format(projectDir))
# Read the Cluster simulation
cp = NepidemiXConfigParser()
with open(projectDir +'/' + ClusterSimulation.original_config_file_name, 'r') as fp:
cp.readfp(fp)
return cp
def createSimulationConfigs(self):
"""
Tailor build individual configurations for each simulation case.
"""
# Go through all settings options. Those not belonging to this
# class is assumed to belong to the program we want to deploy.
logger.info("Building parameter lists...")
paramRangeList, varOptList \
= buildParamRangeList(self.settings,
excludeSections = self.exclude_sections,
excludeOptions = self.exclude_options,
ignoreSections = self.ignore_sections,
ignoreOptions = self.ignore_options)
logger.info("Creating project directory at '{0}'".format(self.projectDirPath))
os.makedirs(self.projectDirPath)
ncalls = 0
deployScriptName = self.projectDirPath +'/' + self.deployScriptName
logger.info("Creating deploy script '{0}'".format(deployScriptName))
deployScriptFp = open(deployScriptName, 'w')
deployScriptFp.write("""
#!/bin/bash
# This script is automatically generated.
# Running it will submit all generated PBS jobs to the queue.
""")
for ddict, cpath in paramsPaths(self.projectDirPath,
paramRangeList, self.confDirName,
excludeSections = self.exclude_sections,
excludeOptions = self.exclude_options,
ignoreSections = self.ignore_sections,
ignoreOptions = self.ignore_options):
cp = NepidemiXConfigParser()
os.makedirs(cpath, 0750)
fname = cpath + "/{0}_{1}".format(self.fileBaseName, ncalls)
# Write ini file.
with open(fname+'.ini', 'w') as fp:
for (sec, opt), val in ddict.items():
if not cp.has_section(sec):
cp.add_section(sec)
cp.set(sec,opt,val)
cp.write(fp)
queue_name = self.settings.get(self.CFG_SECTION_PBS,
self.CFG_PARAM_queue,
default = '')
if len(queue_name) < 1:
queue_string = ""
else:
queue_string ="#PBS -q {queue_name}".format(queue_name=queue_name)
# Write PBS file.
with open(fname+'.pbs', 'w') as fp:
# Header, email and output.
fp.write("""
#!/bin/bash
#PBS -N {job_name}
{queue_string}
#PBS -M {user_email}
#PBS -m bae
#PBS -j oe
#PBS -o {path_to_log}
#PBS -e {path_to_elog}
""".format(job_name = self.projectName + "_{0}".format(ncalls),
queue_string = queue_string,
user_email = self.settings.get(self.CFG_SECTION_PBS,
self.CFG_PARAM_email),
path_to_log = fname+'.log',
path_to_elog = fname+'_error.log'))
# Write -l options.
if self.settings.has_option(self.CFG_SECTION_PBS,
self.CFG_PARAM_pbslopts) == True:
for los in self.settings.\
parseTuple(self.settings.get(self.CFG_SECTION_PBS,
self.CFG_PARAM_pbslopts)):
fp.write("#PBS -l {0}\n".format(los))
# Write the execution commands.
fp.write("""
cd {work_dir}
{command}
""".format(work_dir = cpath,
command = self.simprogram+" {0}.ini {1}".format(fname, self.reps)))
# Add a command to submit the pbs file to our deployment script.
deployScriptFp.write("qsub {0}.pbs; sleep 0.2\n".format(fname))
ncalls = ncalls + 1
deployScriptFp.close()
# Make deploy script executable for user.
os.chmod(deployScriptName, 0744)
self.settings.set(self.CFG_SECTION_INFO, self.CFG_PARAM_num_configs,
ncalls)
self.settings.set(self.CFG_SECTION_INFO, self.CFG_PARAM_config_base_name,
self.fileBaseName)
self.settings.set(self.CFG_SECTION_INFO, self.CFG_PARAM_config_dir_name,
self.confDirName)
# Write the (extended) settings backt to file so that the project
# is self contained in some way.
with open(self.projectDirPath + '/{0}'.format(self.original_config_file_name), 'w') as ofp:
self.settings.write(ofp)
logger.info("Done, created {0} individual configurations to be repeated {1} times."\
.format(ncalls, self.reps))
