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# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under the Lesser GNU Public Licence, v2.1 or any higher version
#
# Please cite your use of MDAnalysis in published work:
#
# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler,
# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein.
# MDAnalysis: A Python package for the rapid analysis of molecular dynamics
# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th
# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy.
#
# N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein.
# MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
#
import numpy as np
import pytest
from numpy.testing import assert_equal
from threadpoolctl import threadpool_info
import MDAnalysis as mda
from MDAnalysisTests.datafiles import PSF, DCD
from MDAnalysis.transformations.base import TransformationBase
class DefaultTransformation(TransformationBase):
"""Default values for max_threads and parallelizable"""
def __init__(self):
super().__init__()
def _transform(self, ts):
self.runtime_info = threadpool_info()
ts.positions = ts.positions + 1
return ts
class NoTransform_Transformation(TransformationBase):
"""Default values for max_threads and parallelizable"""
def __init__(self):
super().__init__()
class CustomTransformation(TransformationBase):
"""Custom value for max_threads and parallelizable"""
def __init__(self, max_threads=1, parallelizable=False):
super().__init__(
max_threads=max_threads, parallelizable=parallelizable
)
def _transform(self, ts):
self.runtime_info = threadpool_info()
ts.positions = ts.positions + 1
return ts
@pytest.fixture(scope="module")
def u():
return mda.Universe(PSF, DCD)
def test_default_value():
new_trans = DefaultTransformation()
assert new_trans.max_threads is None
assert new_trans.parallelizable is True
def test_no_transform_function(u):
new_trans = NoTransform_Transformation()
with pytest.raises(NotImplementedError, match=r"Only implemented"):
_ = new_trans._transform(u.trajectory.ts)
def test_custom_value():
new_trans = CustomTransformation()
assert new_trans.max_threads == 1
assert new_trans.parallelizable is False
def test_setting_thread_limit_value():
new_trans = CustomTransformation(max_threads=4)
assert new_trans.max_threads == 4
def test_thread_limit_apply(u):
default_thread_info = threadpool_info()
default_num_thread_limit_list = [
thread_info["num_threads"] for thread_info in default_thread_info
]
new_trans = CustomTransformation(max_threads=2)
_ = new_trans(u.trajectory.ts)
for thread_info in new_trans.runtime_info:
assert thread_info["num_threads"] == 2
# test the thread limit is only applied locally.
new_thread_info = threadpool_info()
new_num_thread_limit_list = [
thread_info["num_threads"] for thread_info in new_thread_info
]
assert_equal(default_num_thread_limit_list, new_num_thread_limit_list)
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