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Commit 96ec4dc2 authored by Chichi Lalescu's avatar Chichi Lalescu
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add DNS option to executable script

parent 7cbaa8ee
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bfps/DNS.py
View file @ 96ec4dc2
......@@ -45,12 +45,22 @@ class DNS(_code):
def __init__(
self,
work_dir = './',
simname = 'test',
dns_type = 'NSVE',
fluid_dtype = 'single'):
_code.__init__(self, work_dir = work_dir, simname = simname)
self.dns_type = dns_type
self.name = self.dns_type + '-v' + bfps.__version__
simname = 'test'):
_code.__init__(
self,
work_dir = work_dir,
simname = simname)
self.host_info = {'type' : 'cluster',
'environment' : None,
'deltanprocs' : 1,
'queue' : '',
'mail_address': '',
'mail_events' : None}
self.generate_default_parameters()
return None
def set_precision(
self,
fluid_dtype):
if fluid_dtype in [np.float32, np.float64]:
self.fluid_dtype = fluid_dtype
elif fluid_dtype in ['single', 'double']:
......@@ -62,9 +72,13 @@ class DNS(_code):
if self.rtype == np.float32:
self.ctype = np.dtype(np.complex64)
self.C_field_dtype = 'float'
self.fluid_precision = 'single'
elif self.rtype == np.float64:
self.ctype = np.dtype(np.complex128)
self.C_field_dtype = 'double'
self.fluid_precision = 'double'
return None
def write_src(self):
self.version_message = (
'/***********************************************************************\n' +
'* this code automatically generated by bfps\n' +
......@@ -94,13 +108,22 @@ class DNS(_code):
return main_code< {0} >(argc, argv, fpe);
}}
""".format(self.dns_type + '<{0}>'.format(self.C_field_dtype))
self.host_info = {'type' : 'cluster',
'environment' : None,
'deltanprocs' : 1,
'queue' : '',
'mail_address': '',
'mail_events' : None}
self.generate_default_parameters()
self.includes = '\n'.join(
['#include ' + hh
for hh in self.include_list])
with open(self.name + '.cpp', 'w') as outfile:
outfile.write(self.version_message + '\n\n')
outfile.write(self.includes + '\n\n')
outfile.write(self.cread_pars(
template_class = '{0}<rnumber>::'.format(self.dns_type),
template_prefix = 'template <typename rnumber> ',
simname_variable = 'simname.c_str()') + '\n\n')
for rnumber in ['float', 'double']:
outfile.write(self.cread_pars(
template_class = '{0}<{1}>::'.format(self.dns_type, rnumber),
template_prefix = 'template '.format(rnumber),
just_declaration = True) + '\n\n')
outfile.write(self.main + '\n')
return None
def generate_default_parameters(self):
# these parameters are relevant for all DNS classes
......@@ -123,30 +146,12 @@ class DNS(_code):
self.parameters['max_velocity_estimate'] = float(1)
self.parameters['max_vorticity_estimate'] = float(1)
# parameters specific to particle version
if self.dns_type == 'NSVEp':
self.parameters['niter_part'] = int(1)
self.parameters['nparticles'] = int(10)
self.parameters['tracers0_integration_steps'] = int(4)
self.parameters['tracers0_neighbours'] = int(1)
self.parameters['tracers0_smoothness'] = int(1)
return None
def write_src(self):
self.includes = '\n'.join(
['#include ' + hh
for hh in self.include_list])
with open(self.name + '.cpp', 'w') as outfile:
outfile.write(self.version_message + '\n\n')
outfile.write(self.includes + '\n\n')
outfile.write(self.cread_pars(
template_class = '{0}<rnumber>::'.format(self.dns_type),
template_prefix = 'template <typename rnumber> ',
simname_variable = 'simname.c_str()') + '\n\n')
for rnumber in ['float', 'double']:
outfile.write(self.cread_pars(
template_class = '{0}<{1}>::'.format(self.dns_type, rnumber),
template_prefix = 'template '.format(rnumber),
just_declaration = True) + '\n\n')
outfile.write(self.main + '\n')
self.NSVEp_extra_parameters = {}
self.NSVEp_extra_parameters['niter_part'] = int(1)
self.NSVEp_extra_parameters['nparticles'] = int(10)
self.NSVEp_extra_parameters['tracers0_integration_steps'] = int(4)
self.NSVEp_extra_parameters['tracers0_neighbours'] = int(1)
self.NSVEp_extra_parameters['tracers0_smoothness'] = int(1)
return None
def get_kspace(self):
kspace = {}
......@@ -376,7 +381,6 @@ class DNS(_code):
for k in vec_stat_datasets:
time_chunk = 2**20//(8*3*3*nshells)
time_chunk = max(time_chunk, 1)
print(ofile)
ofile.create_dataset('statistics/spectra/' + k + '_' + k,
(1, nshells, 3, 3),
chunks = (time_chunk, nshells, 3, 3),
......@@ -434,10 +438,71 @@ class DNS(_code):
(3,)),
dtype = np.float)
return None
def specific_parser_arguments(
def job_parser_arguments(
self,
parser):
_code.specific_parser_arguments(self, parser)
parser.add_argument(
'--ncpu',
type = int,
dest = 'ncpu',
default = -1)
parser.add_argument(
'--np', '--nprocesses',
metavar = 'NPROCESSES',
help = 'number of mpi processes to use',
type = int,
dest = 'nb_processes',
default = 4)
parser.add_argument(
'--ntpp', '--nthreads-per-process',
type = int,
dest = 'nb_threads_per_process',
metavar = 'NTHREADS_PER_PROCESS',
help = 'number of threads to use per MPI process',
default = 1)
parser.add_argument(
'--no-submit',
action = 'store_true',
dest = 'no_submit')
parser.add_argument(
'--environment',
type = str,
dest = 'environment',
default = None)
parser.add_argument(
'--minutes',
type = int,
dest = 'minutes',
default = 5,
help = 'If environment supports it, this is the requested wall-clock-limit.')
parser.add_argument(
'--njobs',
type = int, dest = 'njobs',
default = 1)
return None
def simulation_parser_arguments(
self,
parser):
parser.add_argument(
'--simname',
type = str, dest = 'simname',
default = 'test')
parser.add_argument(
'-n', '--cube-size',
type = int,
dest = 'n',
default = 32,
metavar = 'N',
help = 'code is run by default in a grid of NxNxN')
parser.add_argument(
'--wd',
type = str, dest = 'work_dir',
default = './')
parser.add_argument(
'--precision',
choices = ['single', 'double'],
type = str,
default = 'single')
parser.add_argument(
'--src-wd',
type = str,
......@@ -453,10 +518,6 @@ class DNS(_code):
type = int,
dest = 'src_iteration',
default = 0)
parser.add_argument(
'--njobs',
type = int, dest = 'njobs',
default = 1)
parser.add_argument(
'--kMeta',
type = float,
......@@ -468,6 +529,10 @@ class DNS(_code):
dest = 'dtfactor',
default = 0.5,
help = 'dt is computed as DTFACTOR / N')
return None
def particle_parser_arguments(
self,
parser):
parser.add_argument(
'--particle-rand-seed',
type = int,
......@@ -503,6 +568,31 @@ class DNS(_code):
dest = 'smoothness',
default = 1)
return None
def add_parser_arguments(
self,
parser):
subparsers = parser.add_subparsers(
dest = 'DNS_class',
help = 'type of simulation to run')
subparsers.required = True
parser_NSVE = subparsers.add_parser(
'NSVE',
help = 'plain Navier-Stokes vorticity formulation')
self.simulation_parser_arguments(parser_NSVE)
self.job_parser_arguments(parser_NSVE)
self.parameters_to_parser_arguments(parser_NSVE)
parser_NSVEp = subparsers.add_parser(
'NSVEp',
help = 'plain Navier-Stokes vorticity formulation, with basic fluid tracers')
self.simulation_parser_arguments(parser_NSVEp)
self.job_parser_arguments(parser_NSVEp)
self.particle_parser_arguments(parser_NSVEp)
self.parameters_to_parser_arguments(parser_NSVEp)
self.parameters_to_parser_arguments(
parser_NSVEp,
self.NSVEp_extra_parameters)
return None
def prepare_launch(
self,
args = []):
......@@ -532,6 +622,13 @@ class DNS(_code):
"""
opt = _code.prepare_launch(self, args = args)
self.set_precision(opt.precision)
self.dns_type = opt.DNS_class
self.name = self.dns_type + '-' + self.fluid_precision + '-v' + bfps.__version__
# merge parameters if needed
if self.dns_type == 'NSVEp':
for k in self.NSVEp_extra_parameters.keys():
self.parameters[k] = self.NSVEp_extra_parameters[k]
self.parameters['nu'] = (opt.kMeta * 2 / opt.n)**(4./3)
self.parameters['dt'] = (opt.dtfactor / opt.n)
# custom famplitude for 288 and 576
......
bfps/__main__.py
View file @ 96ec4dc2
......@@ -28,6 +28,7 @@ import sys
import argparse
import bfps
from .DNS import DNS
from .NavierStokes import NavierStokes
from .NSVorticityEquation import NSVorticityEquation
from .FluidResize import FluidResize
......@@ -64,13 +65,22 @@ def main():
'NSManyParticles-double']
parser.add_argument(
'base_class',
choices = NSoptions + NSVEoptions + FRoptions + FCoptions + NSMPopt,
choices = ['DNS'] +
NSoptions +
NSVEoptions +
FRoptions +
FCoptions +
NSMPopt,
type = str)
# first option is the choice of base class or -h or -v
# all other options are passed on to the base_class instance
opt = parser.parse_args(sys.argv[1:2])
# error is thrown if first option is not a base class, so launch
# cannot be executed by mistake.
if opt.base_class == 'DNS':
c = DNS()
c.launch(args = sys.argv[2:])
return None
if 'double' in opt.base_class:
precision = 'double'
else:
......
tests/test_DNS.py
View file @ 96ec4dc2
......@@ -2,12 +2,13 @@ from bfps.DNS import DNS
def main():
niterations = 16
nparticles = 100
c = DNS(dns_type = 'NSVEp')
niterations = 32
nparticles = 10000
c = DNS()
c.launch(
['-n', '32',
'--simname', 'vorticity_equation',
['NSVEp',
'-n', '32',
'--simname', 'dns_nsvep',
'--np', '4',
'--ntpp', '1',
'--niter_todo', '{0}'.format(niterations),
......@@ -16,7 +17,7 @@ def main():
'--checkpoints_per_file', '{0}'.format(3),
'--nparticles', '{0}'.format(nparticles),
'--particle-rand-seed', '2',
#'--njobs', '2',
'--njobs', '2',
'--wd', './'])
return None
......
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