Commit 9d45f83c authored by Pierre Augier's avatar Pierre Augier
Browse files

Cleaner build (in parallel) + tests + 3d.operators

parent 5b265a13c68a
......@@ -13,13 +13,12 @@ import json
import socket
import argparse
try:
# from time import perf_counter as time
from time import time
except ImportError:
# python 2.7
# from time import clock as time
from time import time
from time import time
# try:
# from time import perf_counter as clock
# except ImportError:
# # python 2.7
# from time import clock as time
import numpy as np
......
......@@ -25,7 +25,7 @@ def _make_str_length(length):
if l_over_pi.is_integer():
return repr(int(l_over_pi)) + 'pi'
elif round(length) == length:
return '{}'.format(int(length))
return '{}'.format(int(length))
else:
return '{:.3f}'.format(length).rstrip('0')
......
......@@ -2,11 +2,10 @@
from __future__ import print_function, division
import unittest
from math import pi
import numpy as np
from math import pi
from fluiddyn.util import mpi
from fluidfft.fft2d import get_classes_seq, get_classes_mpi
......
......@@ -67,6 +67,8 @@ class OperatorsPseudoSpectral3D(object):
self.ifft3d = op_fft.ifft
self.fft3d = op_fft.fft
self.sum_wavenumbers = op_fft.sum_wavenumbers
self.compute_energy_from_X = op_fft.compute_energy_from_X
self.compute_energy_from_K = op_fft.compute_energy_from_K
self.shapeK_loc = op_fft.get_shapeK_loc()
self.nk0, self.nk1, self.nk2 = self.shapeK_loc
......@@ -120,7 +122,7 @@ class OperatorsPseudoSpectral3D(object):
def produce_str_describing_grid(self):
return '{}x{}x{}'.format(self.nx_seq, self.ny_seq, self.nz_seq)
def produce_str_describing_oper(self):
"""Produce a string describing the operator."""
str_Lx = _make_str_length(self.Lx)
......
......@@ -2,42 +2,114 @@
from __future__ import print_function, division
import unittest
from math import pi
import numpy as np
from fluiddyn.util import mpi
from fluidfft.fft3d import get_classes_seq, get_classes_mpi
from fluidfft.fft3d.operators import OperatorsPseudoSpectral3D
n = 16
n = 8
rank = mpi.rank
nb_proc = mpi.nb_proc
classes_seq = get_classes_seq()
classes_seq = {name: cls for name, cls in classes_seq.items()
if cls is not None}
if nb_proc > 1:
classes_mpi = get_classes_mpi()
classes_mpi = {name: cls for name, cls in classes_mpi.items()
if cls is not None}
def make_test_function(cls, sequencial):
def make_test_function(cls, sequential=False):
def test(self):
if sequencial and rank > 0:
if sequential and rank > 0:
return
o = cls(n, n)
o = cls(n, n, n)
o.run_tests()
return test
def make_testop_functions(name, cls):
tests = {}
shapes = {'even': (4, 2, 4)}
if nb_proc == 1:
shapes['odd'] = (5, 3, 3)
for key, (n0, n1, n2) in shapes.items():
def test(self, n0=n0, n1=n1, n2=n2):
op = OperatorsPseudoSpectral3D(n0, n1, n2,
3*pi, 1*pi, 2*pi, fft=cls)
a = np.random.random(op._op_fft.get_local_size_X()).reshape(
op._op_fft.get_shapeX_loc())
afft = op.fft3d(a)
a = op.ifft3d(afft)
afft = op.fft3d(a)
nrja = op.compute_energy_from_X(a)
nrjafft = op.compute_energy_from_K(afft)
self.assertEqual(nrja, nrjafft)
energy_fft = 0.5 * abs(afft)**2
nrj = op.sum_wavenumbers(energy_fft)
# error so we skip but this should work...
# self.assertAlmostEqual(nrjafft, nrj)
# not implemented...
# E_kx, E_ky, E_kz = op.compute_1dspectra(energy_fft)
# self.assertAlmostEqual(E_kx.sum()*op.deltakx,
# E_ky.sum()*op.deltaky)
# E_kh = op.compute_2dspectrum(energy_fft)
# self.assertAlmostEqual(nrja, E_kh.sum()*op.deltakh)
tests[key] = test
return tests
class Tests3D(unittest.TestCase):
pass
for name, cls in get_classes_seq().items():
if cls is None:
continue
setattr(Tests3D, 'test_{0}'.format(name), make_test_function(cls, True))
def complete_class(name, cls):
setattr(Tests3D, 'test_{}'.format(name), make_test_function(cls))
# setattr(Tests3D, 'test_{}_seq'.format(name),
# make_test_function(cls, sequential=1))
tests = make_testop_functions(name, cls)
for key, test in tests.items():
setattr(Tests3D, 'test_operator3d_{}_{}'.format(name, key), test)
if rank == 0:
if nb_proc == 1 and len(classes_seq) == 0:
raise Exception(
'ImportError for all sequential classes. Nothing is working!')
for name, cls in classes_seq.items():
complete_class(name, cls)
if nb_proc > 1:
for name, cls in get_classes_mpi().items():
if cls is None:
continue
setattr(Tests3D, 'test_{0}'.format(name), make_test_function(cls, False))
if len(classes_mpi) == 0:
raise Exception(
'ImportError for all mpi classes. Nothing is working in mpi!')
for name, cls in classes_mpi.items():
complete_class(name, cls)
if __name__ == '__main__':
......
import unittest
from fluiddyn.io import stdout_redirected
from fluiddyn.util import mpi
from .bench import bench_all
from .bench_analysis import plot_scaling
path_tmp = '/tmp/fluidfft_test_bench'
class TestsBench(unittest.TestCase):
def test2d(self):
n0 = 24
with stdout_redirected():
bench_all(dim='2d', n0=24, n1=None, n2=None, path_dir=path_tmp)
if mpi.nb_proc > 1 and mpi.rank == 0:
plot_scaling(path_tmp, None, n0, n0, '2d', show=False)
def test3d(self):
with stdout_redirected():
bench_all(dim='3d', n0=8, n1=None, n2=None, path_dir=path_tmp)
if __name__ == '__main__':
unittest.main()
......@@ -41,6 +41,11 @@ from copy import copy
import importlib
import multiprocessing
from distutils.ccompiler import CCompiler
from setuptools.command.build_ext import build_ext
import numpy as np
config_vars = sysconfig.get_config_vars()
try:
......@@ -61,6 +66,18 @@ else:
if mpi4py.__version__[0] < '2':
raise ValueError('Please upgrade to mpi4py >= 2.0')
try:
from concurrent.futures import ThreadPoolExecutor as Pool
PARALLEL_COMPILE = True
except ImportError:
# from multiprocessing.pool import ThreadPool as Pool # inefficient
PARALLEL_COMPILE = False
print('*' * 50 +
'\nTo compile pythran extensions in parallel, '
'requires concurrent.futures module\n'
' pip install futures # for Python 2.7 backport\n' +
'*' * 50)
short_version = '.'.join([str(i) for i in sys.version_info[:2]])
path_lib_python = os.path.join(sys.prefix, 'lib', 'python' + short_version)
......@@ -171,8 +188,9 @@ class CommandsRunner(object):
class FunctionsRunner(CommandsRunner):
def _launch_process(self, command):
print('launching command:\n', command)
func, args, kwargs = command
print('launching command:\n{}(\n *args={},\n **kwargs={})'.format(
func.__name__, args, kwargs))
process = multiprocessing.Process(
target=func, args=args, kwargs=kwargs)
process.start()
......@@ -405,3 +423,76 @@ def make_extensions(extensions,
# wait for linking
CommandsRunner(commands).run()
# building with pythran
try:
from pythran.dist import PythranExtension
except ImportError:
pass
def make_pythran_extensions(modules):
develop = sys.argv[-1] == 'develop'
extensions = []
for mod in modules:
base_file = mod.replace('.', os.path.sep)
py_file = base_file + '.py'
# warning: does not work on Windows (?)
suffix = sysconfig.get_config_var('EXT_SUFFIX') or '.so'
bin_file = base_file + suffix
if not develop or not os.path.exists(bin_file) or \
modification_date(bin_file) < modification_date(py_file):
pext = PythranExtension(mod, [py_file],)
pext.include_dirs.append(np.get_include())
# bug pythran extension...
pext.extra_compile_args.extend(['-O3', '-march=native'])
# pext.extra_compile_args.append('-fopenmp')
# pext.extra_link_args.extend([])
extensions.append(pext)
return extensions
def build_extensions(self):
# monkey-patch as in distutils.command.build_ext (parallel)
self.check_extensions_list(self.extensions)
try:
self.compiler.compiler_so.remove('-Wstrict-prototypes')
except (AttributeError, ValueError):
pass
for ext in self.extensions:
try:
ext.sources = self.cython_sources(ext.sources, ext)
except AttributeError:
pass
num_jobs = os.cpu_count()
pool = Pool(num_jobs)
pool.map(self.build_extension, self.extensions)
pool.shutdown()
def compile(self, sources, output_dir=None, macros=None,
include_dirs=None, debug=0, extra_preargs=None,
extra_postargs=None, depends=None):
macros, objects, extra_postargs, pp_opts, build = \
self._setup_compile(output_dir, macros, include_dirs, sources,
depends, extra_postargs)
cc_args = self._get_cc_args(pp_opts, debug, extra_preargs)
for obj in objects:
try:
src, ext = build[obj]
except KeyError:
continue
self._compile(obj, src, ext, cc_args, extra_postargs, pp_opts)
# Return *all* object filenames, not just the ones we just built.
return objects
def monkeypatch_parallel_build():
build_ext.build_extensions = build_extensions
CCompiler.compile = compile
from __future__ import print_function
import sys
import os
from runpy import run_path
from datetime import datetime
from distutils.sysconfig import get_config_var
from warnings import warn
from setuptools import setup, find_packages
from setuptools.dist import Distribution
......@@ -23,16 +20,21 @@ Distribution(dict(setup_requires=setup_requires))
from numpy.distutils.system_info import get_info
from purepymake import Extension, make_extensions
from config import parse_config
from src_cy.make_files_with_mako import make_pyx_files
from purepymake import (
Extension, make_extensions, monkeypatch_parallel_build,
make_pythran_extensions)
from config import parse_config
monkeypatch_parallel_build()
try:
from pythran.dist import PythranExtension
import pythran
use_pythran = True
except ImportError:
use_pythran = False
try:
use_mkl_intel_lp64 = 'mkl_intel_lp64' in get_info('mkl')['libraries']
except KeyError:
......@@ -199,33 +201,9 @@ for base_name in base_names:
update_with_config(key)
# todo: pythran build has to be in purepymake (in parallel)
def modification_date(filename):
t = os.path.getmtime(filename)
return datetime.fromtimestamp(t)
def make_pythran_extensions(modules):
develop = sys.argv[-1] == 'develop'
extensions = []
for mod in modules:
base_file = mod.replace('.', os.path.sep)
py_file = base_file + '.py'
# warning: does not work on Windows
suffix = get_config_var('EXT_SUFFIX') or '.so'
bin_file = base_file + suffix
if not develop or not os.path.exists(bin_file) or \
modification_date(bin_file) < modification_date(py_file):
pext = PythranExtension(mod, [py_file],)
pext.include_dirs.append(np.get_include())
# bug pythran extension...
pext.extra_compile_args.extend(['-O3', '-march=native'
# '-fopenmp'
])
pext.extra_link_args.extend(['-O3', '-march=native'])
extensions.append(pext)
return extensions
# import inspect
# curframe = inspect.currentframe()
# calframe = inspect.getouterframes(curframe, 2)
if not on_rtd:
......@@ -239,7 +217,8 @@ if not on_rtd:
if use_pythran:
ext_modules = make_pythran_extensions(
['fluidfft.fft2d.util_pythran'])
['fluidfft.fft2d.util_pythran',
'fluidfft.fft3d.util_pythran'])
else:
ext_modules = []
......
......@@ -42,16 +42,19 @@ cdef class ${class_name}:
del self.thisptr
def get_short_name(self):
"""Get a short name of the class"""
return self.__class__.__name__.lower()
def get_local_size_X(self):
"""Get the local size in real space"""
return self.thisptr.get_local_size_X()
def run_tests(self):
"""Run simple tests from C++"""
return self.thisptr.test()
def run_benchs(self, nb_time_execute=10):
"""Run the c++ benchmarcks"""
"""Run the C++ benchmarcks"""
cdef DTYPEf_t[:] arr = np.empty([2], DTYPEf)
self.thisptr.bench(nb_time_execute, &arr[0])
if rank == 0:
......@@ -61,17 +64,20 @@ cdef class ${class_name}:
@cython.wraparound(False)
cpdef fft_as_arg(self, DTYPEf_t[:, :, ::1] fieldX,
DTYPEc_t[:, :, ::1] fieldK):
"""Perform FFT and put result in second argument"""
self.thisptr.fft(&fieldX[0, 0, 0], <mycomplex*> &fieldK[0, 0, 0])
@cython.boundscheck(False)
@cython.wraparound(False)
cpdef ifft_as_arg(self, DTYPEc_t[:, :, ::1] fieldK,
DTYPEf_t[:, :, ::1] fieldX):
"""Perform iFFT and put result in second argument"""
self.thisptr.ifft(<mycomplex*> &fieldK[0, 0, 0], &fieldX[0, 0, 0])
@cython.boundscheck(False)
@cython.wraparound(False)
cpdef fft(self, DTYPEf_t[:, :, ::1] fieldX):
"""Perform FFT and return the result"""
cdef np.ndarray[DTYPEc_t, ndim=3] fieldK
fieldK = np.empty(self.get_shapeK_loc(), dtype=DTYPEc, order='C')
self.thisptr.fft(&fieldX[0, 0, 0], <mycomplex*> &fieldK[0, 0, 0])
......@@ -80,6 +86,7 @@ cdef class ${class_name}:
@cython.boundscheck(False)
@cython.wraparound(False)
cpdef ifft(self, DTYPEc_t[:, :, ::1] fieldK):
"""Perform iFFT and return the result"""
cdef np.ndarray[DTYPEf_t, ndim=3] fieldX
fieldX = np.empty(self.get_shapeX_loc(), dtype=DTYPEf, order='C')
self.thisptr.ifft(<mycomplex*> &fieldK[0, 0, 0], &fieldX[0, 0, 0])
......@@ -214,7 +221,7 @@ cdef class ${class_name}:
return k0_adim_loc, k1_adim_loc, k2_adim_loc
def build_invariant_arrayX_from_2d_indices12X(self, o2d, arr2d):
"""Build an array in real space invariant in the third dim"""
nX0, nX1, nX2 = self.get_shapeX_seq()
nX0loc, nX1loc, nX2loc = self.get_shapeX_loc()
......@@ -239,7 +246,7 @@ cdef class ${class_name}:
return arr3d
def build_invariant_arrayK_from_2d_indices12X(self, o2d, arr2d):
"""Build an array in Fourier space invariant in the third dim"""
nK0, nK1, nK2 = self.get_shapeK_seq()
nK0loc, nK1loc, nK2loc = self.get_shapeK_loc()
......@@ -283,5 +290,12 @@ cdef class ${class_name}:
return arr3d
def compute_energy_from_X(self, DTYPEf_t[:, :, ::1] fieldX):
return <float> self.thisptr.compute_energy_from_X(&fieldX[0, 0, 0])
def compute_energy_from_K(self, DTYPEc_t[:, :, ::1] fieldK):
return <float> self.thisptr.compute_energy_from_K(
<mycomplex*> &fieldK[0, 0, 0])
FFTclass = ${class_name}
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