From 96ec4dc2567b51d3bd457bec553893bf755fb10b Mon Sep 17 00:00:00 2001
From: Chichi Lalescu <chichilalescu@gmail.com>
Date: Thu, 4 May 2017 22:46:25 +0200
Subject: [PATCH] add DNS option to executable script
---
bfps/DNS.py | 185 +++++++++++++++++++++++++++++++++++-----------
bfps/__main__.py | 12 ++-
tests/test_DNS.py | 13 ++--
3 files changed, 159 insertions(+), 51 deletions(-)
diff --git a/bfps/DNS.py b/bfps/DNS.py
index b90c6d46..0d8571b0 100644
--- a/bfps/DNS.py
+++ b/bfps/DNS.py
@@ -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
diff --git a/bfps/__main__.py b/bfps/__main__.py
index 9db5e350..f1ee7278 100644
--- a/bfps/__main__.py
+++ b/bfps/__main__.py
@@ -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:
diff --git a/tests/test_DNS.py b/tests/test_DNS.py
index 4e8cb2f8..9169cef9 100644
--- a/tests/test_DNS.py
+++ b/tests/test_DNS.py
@@ -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
--
GitLab