def load_sites(parallel, load_dir):
"""
Load the site object from file in load_dir
"""
log.info('P%s: Loading site from %s' % (parallel.rank, load_dir))
sites = Sites.load(load_dir)
return sites
def load_sites(parallel, load_dir):
"""
Load the site object from file in load_dir
"""
log.info('P%s: Loading site from %s' % (parallel.rank, load_dir))
sites = Sites.load(load_dir)
return sites
def log_analysis():
'''log_analysis - analyses the current log and returns a tuple list containing
- Memory usage 'event' key
- Memory usage data value
It makes the assumption that the current pattern for logging memory usage
is consistent. e.g.
log.debug('Memory: event_set_zone created')
log.resource_usage()
This will produce lines in the log file that looks like
2012-01-12 13:12:29,694 DEBUG analysis:228 |Memory: event_set_zone created
2012-01-12 13:12:29,695 DEBUG analysis:229 |Resource usage: memory=1151.0MB resident=758.2MB stacksize=0.3MB
What we want from this example is a tuple that looks like
('event_set_zone created', 'memory=1151.0MB resident=758.2MB stacksize=0.3MB')
Where the 'event' key is the 'Memory:' log reference and the data value is the
'Resource usage:' log reference.
'''
results = []
# Only do this is the logfile exists
if os.path.exists(log.log_filename):
# 1. Determine logfile for the previous run
# Note: analysis.main changes the value of log.log_filename per setdata
# file
log.info('log_analysis - using log file %s' % log.log_filename)
log_file = open(log.log_filename)
# 2. Grab the Memory/Resource lines in a tuple
for line in log_file:
if line.find('Memory:') > -1:
key_line = line
value_line = log_file.next()
# This assumes the current pattern will always be
_, key = key_line.split('Memory: ', 1)
_, value = value_line.split('Resource usage: ', 1)
# We want to preserve order so cannot use a dict
results.append((key.strip(), value.strip()))
log_file.close()
# 3. Return tuple array
return results
def log_analysis():
'''log_analysis - analyses the current log and returns a tuple list containing
- Memory usage 'event' key
- Memory usage data value
It makes the assumption that the current pattern for logging memory usage
is consistent. e.g.
log.debug('Memory: event_set_zone created')
log.resource_usage()
This will produce lines in the log file that looks like
2012-01-12 13:12:29,694 DEBUG analysis:228 |Memory: event_set_zone created
2012-01-12 13:12:29,695 DEBUG analysis:229 |Resource usage: memory=1151.0MB resident=758.2MB stacksize=0.3MB
What we want from this example is a tuple that looks like
('event_set_zone created', 'memory=1151.0MB resident=758.2MB stacksize=0.3MB')
Where the 'event' key is the 'Memory:' log reference and the data value is the
'Resource usage:' log reference.
'''
results = []
# Only do this is the logfile exists
if os.path.exists(log.log_filename):
# 1. Determine logfile for the previous run
# Note: analysis.main changes the value of log.log_filename per setdata
# file
log.info('log_analysis - using log file %s' % log.log_filename)
log_file = open(log.log_filename)
# 2. Grab the Memory/Resource lines in a tuple
for line in log_file:
if line.find('Memory:') > -1:
key_line = line
value_line = log_file.next()
# This assumes the current pattern will always be
_, key = key_line.split('Memory: ', 1)
_, value = value_line.split('Resource usage: ', 1)
# We want to preserve order so cannot use a dict
results.append((key.strip(), value.strip()))
log_file.close()
# 3. Return tuple array
return results
events = Event_Set.generate_synthetic_events(
file_name,
fault_width,
azi,
dazi,
fault_dip,
prob_min_mag_cutoff,
override_xml,
prob_number_of_events_in_zones)
# print "events.trace_start_lat", events.trace_start_lat
# print " events.trace_start_lon", events.trace_start_lon
# print "events.trace_end_lat", events.trace_end_lat
# print "events.trace_end_lon", events.trace_end_lon
# print "events.rupture_centroid_lat", events.rupture_centroid_lat
# print "events.rupture_centroid_lon", events.rupture_centroid_lon
# print "events.rupture_centroid_x", events.rupture_centroid_x
# print "events.rupture_centroid_y", events.rupture_centroid_y
os.remove(file_name)
#-------------------------------------------------------------
if __name__ == "__main__":
event_num = 100000
eqrmlog.console_logging_level = eqrmlog.INFO
eqrmlog.info('Memory: before creating ' + str(event_num) + ' events')
eqrmlog.resource_usage(level=eqrmlog.INFO)
create_event_set(event_num)
eqrmlog.info('Memory: after')
eqrmlog.resource_usage(level=eqrmlog.INFO)
def create_nci_job(nodes, param_file):
"""
Creates an NCI job package from the given parameter file and the number of
nodes specified.
"""
# Initial node number validation
if nodes > 8 and nodes % 8 != 0:
raise Exception('Nodes must be a multiple of 8 if greater than 8.')
if nodes > LIMIT_NODES:
raise Exception('The node limit is %s' % LIMIT_NODES)
# Parse param_file to eqrm_flags
eqrm_flags = create_parameter_data(param_file)
# Some validation based on the event_set_handler value
if eqrm_flags.event_set_handler is 'save':
raise Exception(
'Please ensure that event_set_handler is load or generate')
if eqrm_flags.event_set_handler is not 'load':
log.info('')
log.info('event_set_handler not load. Generating event set for NCI.')
log.info('')
# Calculate parameters required for job
params = calc_params(eqrm_flags)
req_memory = calc_memory(nodes, params)
req_jobfs = calc_jobfs(nodes)
req_walltime = calc_walltime(nodes)
# Validation based on parameters
msg = ''
if req_memory > nodes * LIMIT_MEMORY_MULTIPLIER:
msg = '%sRequired memory %sMB greater than limit %sMB.\n' % (
msg, req_memory, nodes * LIMIT_MEMORY_MULTIPLIER)
if req_jobfs > nodes * LIMIT_JOBFS_MULTIPLIER:
msg = '%sRequired jobfs %sMB greater than limit %sMB\n' % (
msg, req_jobfs, nodes * LIMIT_JOBFS_MULTIPLIER)
if req_walltime > LIMIT_WALLTIME_MULTIPLIER(nodes):
msg = '%sRequired walltime %ssecs greater than limit %ssecs\n' % (
msg, req_walltime, LIMIT_WALLTIME_MULTIPLIER(nodes))
if len(msg) > 0:
msg += 'Consider reducing the size of your simulation.'
raise Exception(msg)
# Create directory to package into
nci_dir = os.path.join('.', 'nci_job')
if os.path.exists(nci_dir):
rmtree(nci_dir)
os.makedirs(nci_dir)
log.info('')
log.info('Saving package to %s' % nci_dir)
log.info('(replaces current directory if exists)')
# Copy input, output and save data to the packaged directory
input_dir = os.path.join(nci_dir, 'input')
copytree(eqrm_flags.input_dir, input_dir)
output_dir = os.path.join(nci_dir, 'output')
if not os.path.exists(output_dir):
os.makedirs(output_dir)
save_dir = os.path.join(nci_dir, 'save')
copytree(
os.path.join(eqrm_flags.output_dir,
'%s_event_set' % eqrm_flags.site_tag), save_dir)
# Modify eqrm_flags directories for NCI
eqrm_flags['input_dir'] = os.path.join('.', 'input')
eqrm_flags['output_dir'] = os.path.join('.', 'output')
eqrm_flags['data_array_storage'] = "getenv('PBS_JOBFS')"
eqrm_flags['event_set_load_dir'] = os.path.join('.', 'save')
# We always want a load job
eqrm_flags['event_set_handler'] = "load"
# Write new setdata file
eqrm_flags_to_control_file(os.path.join(nci_dir, param_file), eqrm_flags)
# Write NCI job file
job_file = open(os.path.join(nci_dir, '%s_job' % param_file), 'w')
job_file.write('#!/bin/bash\n')
job_file.write('#PBS -wd\n')
job_file.write('#PBS -q normal\n')
job_file.write('#PBS -l ncpus=%s\n' % nodes)
job_file.write('#PBS -l walltime=%s\n' % req_walltime)
job_file.write('#PBS -l vmem=%sMB\n' % req_memory)
job_file.write('#PBS -l jobfs=%sMB\n' % req_jobfs)
job_file.write('\n')
job_file.write('mpirun python %s\n' % param_file)
job_file.close()
log.info('')
log.info('Now tar gzip %s and copy to NCI. e.g.' % nci_dir)
log.info('tar czvf nci_job.tar.gz %s' % nci_dir)
log.info('scp nci_job.tar.gz <username>@<nci_host>:/short/<project>/jobs/')
log.info('')
def logMessages(self):
log.debug('test at level DEBUG')
log.info('test at level INFO')
log.warning('test at level WARNING')
log.error('test at level ERROR')
log.critical('test at level CRITICAL')
def create_nci_job(nodes, param_file):
"""
Creates an NCI job package from the given parameter file and the number of
nodes specified.
"""
# Initial node number validation
if nodes > 8 and nodes % 8 != 0:
raise Exception('Nodes must be a multiple of 8 if greater than 8.')
if nodes > LIMIT_NODES:
raise Exception('The node limit is %s' % LIMIT_NODES)
# Parse param_file to eqrm_flags
eqrm_flags = create_parameter_data(param_file)
# Some validation based on the event_set_handler value
if eqrm_flags.event_set_handler is 'save':
raise Exception('Please ensure that event_set_handler is load or generate')
if eqrm_flags.event_set_handler is not 'load':
log.info('')
log.info('event_set_handler not load. Generating event set for NCI.')
log.info('')
# Calculate parameters required for job
params = calc_params(eqrm_flags)
req_memory = calc_memory(nodes, params)
req_jobfs = calc_jobfs(nodes)
req_walltime = calc_walltime(nodes)
# Validation based on parameters
msg = ''
if req_memory > nodes * LIMIT_MEMORY_MULTIPLIER:
msg = '%sRequired memory %sMB greater than limit %sMB.\n' % (msg,
req_memory,
nodes * LIMIT_MEMORY_MULTIPLIER)
if req_jobfs > nodes * LIMIT_JOBFS_MULTIPLIER:
msg = '%sRequired jobfs %sMB greater than limit %sMB\n' % (msg,
req_jobfs,
nodes * LIMIT_JOBFS_MULTIPLIER)
if req_walltime > LIMIT_WALLTIME_MULTIPLIER(nodes):
msg = '%sRequired walltime %ssecs greater than limit %ssecs\n' % (msg,
req_walltime,
LIMIT_WALLTIME_MULTIPLIER(nodes))
if len(msg) > 0:
msg += 'Consider reducing the size of your simulation.'
raise Exception(msg)
# Create directory to package into
nci_dir = os.path.join('.', 'nci_job')
if os.path.exists(nci_dir):
rmtree(nci_dir)
os.makedirs(nci_dir)
log.info('')
log.info('Saving package to %s' % nci_dir)
log.info('(replaces current directory if exists)')
# Copy input, output and save data to the packaged directory
input_dir = os.path.join(nci_dir, 'input')
copytree(eqrm_flags.input_dir,input_dir)
output_dir = os.path.join(nci_dir, 'output')
if not os.path.exists(output_dir):
os.makedirs(output_dir)
save_dir = os.path.join(nci_dir, 'save')
copytree(os.path.join(eqrm_flags.output_dir,
'%s_event_set' % eqrm_flags.site_tag), save_dir)
# Modify eqrm_flags directories for NCI
eqrm_flags['input_dir'] = os.path.join('.', 'input')
eqrm_flags['output_dir'] = os.path.join('.', 'output')
eqrm_flags['data_array_storage'] = "getenv('PBS_JOBFS')"
eqrm_flags['event_set_load_dir'] = os.path.join('.', 'save')
# We always want a load job
eqrm_flags['event_set_handler'] = "load"
# Write new setdata file
eqrm_flags_to_control_file(os.path.join(nci_dir, param_file), eqrm_flags)
# Write NCI job file
job_file = open(os.path.join(nci_dir, '%s_job' % param_file), 'w')
job_file.write('#!/bin/bash\n')
job_file.write('#PBS -wd\n')
job_file.write('#PBS -q normal\n')
job_file.write('#PBS -l ncpus=%s\n' % nodes)
job_file.write('#PBS -l walltime=%s\n' % req_walltime)
job_file.write('#PBS -l vmem=%sMB\n' % req_memory)
job_file.write('#PBS -l jobfs=%sMB\n' % req_jobfs)
job_file.write('\n')
job_file.write('mpirun python %s\n' % param_file)
job_file.close()
log.info('')
log.info('Now tar gzip %s and copy to NCI. e.g.' % nci_dir)
log.info('tar czvf nci_job.tar.gz %s' % nci_dir)
log.info('scp nci_job.tar.gz <username>@<nci_host>:/short/<project>/jobs/')
log.info('')
def logMessages(self):
log.debug('test at level DEBUG')
log.info('test at level INFO')
log.warning('test at level WARNING')
log.error('test at level ERROR')
log.critical('test at level CRITICAL')