def __init__(self, funcfile, radius, params,
inputfile, outputfile=None, **extra_args):
funcname = basename_sans(funcfile)
self.funcname = funcname
self.radius = radius
# map args to file system names
inputname = basename_sans(inputfile)
if outputfile is None:
outputfile = ('output_{inputname}_{radius}.mat'.format(**locals()))
# default execution params
extra_args.setdefault('requested_cores', 1)
extra_args.setdefault('requested_memory', 3*GB)
extra_args.setdefault('requested_architecture', Run.Arch.X86_64)
extra_args.setdefault('requested_walltime', 30*days)
# actual app initialization
Application.__init__(
self,
arguments=[
'matlab', '-nodisplay', '-nojvm', #'-singleCompThread',
'-r', (self.matlab_cmd.format(**locals()))
],
inputs = [funcfile, inputfile],
outputs = [outputfile],
stdout = 'matlab.log',
join=True,
**extra_args)
def __init__(self,
funcfile,
radius,
params,
inputfile,
outputfile=None,
**extra_args):
funcname = basename_sans(funcfile)
self.funcname = funcname
self.radius = radius
# map args to file system names
inputname = basename_sans(inputfile)
if outputfile is None:
outputfile = ('output_{inputname}_{radius}.mat'.format(**locals()))
# default execution params
extra_args.setdefault('requested_cores', 1)
extra_args.setdefault('requested_memory', 3 * GB)
extra_args.setdefault('requested_architecture', Run.Arch.X86_64)
extra_args.setdefault('requested_walltime', 30 * days)
# actual app initialization
Application.__init__(
self,
arguments=[
'matlab',
'-nodisplay',
'-nojvm', #'-singleCompThread',
'-r',
(self.matlab_cmd.format(**locals()))
],
inputs=[funcfile, inputfile],
outputs=[outputfile],
stdout='matlab.log',
join=True,
**extra_args)
def new_tasks1(self, funcname, values, inputfiles, **extra):
"""
Iterate over tasks with a common processing function.
"""
# find MATLAB function to run
funcname, funcfile = self.get_function_name_and_file(funcname)
ranges = []
for spec in values.split(','):
# get range for neighborhood radius
low, high, step = parse_range(spec)
ranges.append(irange(low, high+1, step))
for radius in itertools.chain(*ranges):
for inputfile in inputfiles:
kwargs = extra.copy()
base_output_dir = kwargs.pop('output_dir', self.params.output)
inputfile = realpath(inputfile)
inputname = basename_sans(inputfile)
jobname = ('{funcname}_{inputname}_{radius}'.format(**locals()))
outputfile = ('output_{inputname}_{radius}.mat'.format(**locals()))
output_dir = join(base_output_dir, jobname)
yield MatlabRetryOnOutOfMemory(
FunctionalDiversityApplication(
funcfile,
radius,
self.params.parameters,
inputfile,
jobname=jobname,
outputfile=outputfile,
output_dir=output_dir,
**kwargs),
increment=4*GB,
jobname=jobname,
)
def new_tasks1(self, funcname, values, inputfiles, **extra):
"""
Iterate over tasks with a common processing function.
"""
# find MATLAB function to run
funcname, funcfile = self.get_function_name_and_file(funcname)
ranges = []
for spec in values.split(','):
# get range for neighborhood radius
low, high, step = parse_range(spec)
ranges.append(irange(low, high + 1, step))
for radius in itertools.chain(*ranges):
for inputfile in inputfiles:
kwargs = extra.copy()
base_output_dir = kwargs.pop('output_dir', self.params.output)
inputfile = realpath(inputfile)
inputname = basename_sans(inputfile)
jobname = ('{funcname}_{inputname}_{radius}'.format(
**locals()))
outputfile = ('output_{inputname}_{radius}.mat'.format(
**locals()))
output_dir = join(base_output_dir, jobname)
yield MatlabRetryOnOutOfMemory(
FunctionalDiversityApplication(funcfile,
radius,
self.params.parameters,
inputfile,
jobname=jobname,
outputfile=outputfile,
output_dir=output_dir,
**kwargs),
increment=4 * GB,
jobname=jobname,
)
