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{{py:
implementation_specific_values = [
# Values are the following ones:
#
# name_suffix, INPUT_DTYPE_t, INPUT_DTYPE
#
# We also use the float64 dtype and C-type names as defined in
# `sklearn.utils._typedefs` to maintain consistency.
#
('64', 'DTYPE_t', 'DTYPE'),
('32', 'cnp.float32_t', 'np.float32')
]
}}
cimport numpy as cnp
from cython cimport final
from cython.operator cimport dereference as deref
from cython.parallel cimport parallel, prange
from libcpp.vector cimport vector
from ...utils._cython_blas cimport _dot
from ...utils._openmp_helpers cimport _openmp_thread_num
from ...utils._typedefs cimport ITYPE_t, DTYPE_t
import numpy as np
from scipy.sparse import issparse
from numbers import Integral
from sklearn import get_config
from sklearn.utils import check_scalar
from ...utils._openmp_helpers import _openmp_effective_n_threads
from ...utils._typedefs import DTYPE, SPARSE_INDEX_TYPE
cnp.import_array()
#####################
cdef DTYPE_t[::1] _sqeuclidean_row_norms64_dense(
const DTYPE_t[:, ::1] X,
ITYPE_t num_threads,
):
"""Compute the squared euclidean norm of the rows of X in parallel.
This is faster than using np.einsum("ij, ij->i") even when using a single thread.
"""
cdef:
# Casting for X to remove the const qualifier is needed because APIs
# exposed via scipy.linalg.cython_blas aren't reflecting the arguments'
# const qualifier.
# See: https://github.com/scipy/scipy/issues/14262
DTYPE_t * X_ptr = <DTYPE_t *> &X[0, 0]
ITYPE_t idx = 0
ITYPE_t n = X.shape[0]
ITYPE_t d = X.shape[1]
DTYPE_t[::1] squared_row_norms = np.empty(n, dtype=DTYPE)
for idx in prange(n, schedule='static', nogil=True, num_threads=num_threads):
squared_row_norms[idx] = _dot(d, X_ptr + idx * d, 1, X_ptr + idx * d, 1)
return squared_row_norms
cdef DTYPE_t[::1] _sqeuclidean_row_norms32_dense(
const cnp.float32_t[:, ::1] X,
ITYPE_t num_threads,
):
"""Compute the squared euclidean norm of the rows of X in parallel.
This is faster than using np.einsum("ij, ij->i") even when using a single thread.
"""
cdef:
# Casting for X to remove the const qualifier is needed because APIs
# exposed via scipy.linalg.cython_blas aren't reflecting the arguments'
# const qualifier.
# See: https://github.com/scipy/scipy/issues/14262
cnp.float32_t * X_ptr = <cnp.float32_t *> &X[0, 0]
ITYPE_t i = 0, j = 0
ITYPE_t thread_num
ITYPE_t n = X.shape[0]
ITYPE_t d = X.shape[1]
DTYPE_t[::1] squared_row_norms = np.empty(n, dtype=DTYPE)
# To upcast the i-th row of X from float32 to float64
vector[vector[DTYPE_t]] X_i_upcast = vector[vector[DTYPE_t]](
num_threads, vector[DTYPE_t](d)
)
with nogil, parallel(num_threads=num_threads):
thread_num = _openmp_thread_num()
for i in prange(n, schedule='static'):
# Upcasting the i-th row of X from float32 to float64
for j in range(d):
X_i_upcast[thread_num][j] = <DTYPE_t> deref(X_ptr + i * d + j)
squared_row_norms[i] = _dot(
d, X_i_upcast[thread_num].data(), 1,
X_i_upcast[thread_num].data(), 1,
)
return squared_row_norms
cdef DTYPE_t[::1] _sqeuclidean_row_norms64_sparse(
const DTYPE_t[:] X_data,
const SPARSE_INDEX_TYPE_t[:] X_indptr,
ITYPE_t num_threads,
):
cdef:
ITYPE_t n = X_indptr.shape[0] - 1
SPARSE_INDEX_TYPE_t X_i_ptr, idx = 0
DTYPE_t[::1] squared_row_norms = np.zeros(n, dtype=DTYPE)
for idx in prange(n, schedule='static', nogil=True, num_threads=num_threads):
for X_i_ptr in range(X_indptr[idx], X_indptr[idx+1]):
squared_row_norms[idx] += X_data[X_i_ptr] * X_data[X_i_ptr]
return squared_row_norms
{{for name_suffix, INPUT_DTYPE_t, INPUT_DTYPE in implementation_specific_values}}
from ._datasets_pair cimport DatasetsPair{{name_suffix}}
cpdef DTYPE_t[::1] _sqeuclidean_row_norms{{name_suffix}}(
X,
ITYPE_t num_threads,
):
if issparse(X):
# TODO: remove this instruction which is a cast in the float32 case
# by moving squared row norms computations in MiddleTermComputer.
X_data = np.asarray(X.data, dtype=DTYPE)
X_indptr = np.asarray(X.indptr, dtype=SPARSE_INDEX_TYPE)
return _sqeuclidean_row_norms64_sparse(X_data, X_indptr, num_threads)
else:
return _sqeuclidean_row_norms{{name_suffix}}_dense(X, num_threads)
cdef class BaseDistancesReduction{{name_suffix}}:
"""
Base float{{name_suffix}} implementation template of the pairwise-distances
reduction backends.
Implementations inherit from this template and may override the several
defined hooks as needed in order to easily extend functionality with
minimal redundant code.
"""
def __init__(
self,
DatasetsPair{{name_suffix}} datasets_pair,
chunk_size=None,
strategy=None,
):
cdef:
ITYPE_t X_n_full_chunks, Y_n_full_chunks
if chunk_size is None:
chunk_size = get_config().get("pairwise_dist_chunk_size", 256)
self.chunk_size = check_scalar(chunk_size, "chunk_size", Integral, min_val=20)
self.effective_n_threads = _openmp_effective_n_threads()
self.datasets_pair = datasets_pair
self.n_samples_X = datasets_pair.n_samples_X()
self.X_n_samples_chunk = min(self.n_samples_X, self.chunk_size)
X_n_full_chunks = self.n_samples_X // self.X_n_samples_chunk
X_n_samples_remainder = self.n_samples_X % self.X_n_samples_chunk
self.X_n_chunks = X_n_full_chunks + (X_n_samples_remainder != 0)
if X_n_samples_remainder != 0:
self.X_n_samples_last_chunk = X_n_samples_remainder
else:
self.X_n_samples_last_chunk = self.X_n_samples_chunk
self.n_samples_Y = datasets_pair.n_samples_Y()
self.Y_n_samples_chunk = min(self.n_samples_Y, self.chunk_size)
Y_n_full_chunks = self.n_samples_Y // self.Y_n_samples_chunk
Y_n_samples_remainder = self.n_samples_Y % self.Y_n_samples_chunk
self.Y_n_chunks = Y_n_full_chunks + (Y_n_samples_remainder != 0)
if Y_n_samples_remainder != 0:
self.Y_n_samples_last_chunk = Y_n_samples_remainder
else:
self.Y_n_samples_last_chunk = self.Y_n_samples_chunk
if strategy is None:
strategy = get_config().get("pairwise_dist_parallel_strategy", 'auto')
if strategy not in ('parallel_on_X', 'parallel_on_Y', 'auto'):
raise RuntimeError(f"strategy must be 'parallel_on_X, 'parallel_on_Y', "
f"or 'auto', but currently strategy='{self.strategy}'.")
if strategy == 'auto':
# This is a simple heuristic whose constant for the
# comparison has been chosen based on experiments.
# parallel_on_X has less synchronization overhead than
# parallel_on_Y and should therefore be used whenever
# n_samples_X is large enough to not starve any of the
# available hardware threads.
if self.n_samples_Y < self.n_samples_X:
# No point to even consider parallelizing on Y in this case. This
# is in particular important to do this on machines with a large
# number of hardware threads.
strategy = 'parallel_on_X'
elif 4 * self.chunk_size * self.effective_n_threads < self.n_samples_X:
# If Y is larger than X, but X is still large enough to allow for
# parallelism, we might still want to favor parallelizing on X.
strategy = 'parallel_on_X'
else:
strategy = 'parallel_on_Y'
self.execute_in_parallel_on_Y = strategy == "parallel_on_Y"
# Not using less, not using more.
self.chunks_n_threads = min(
self.Y_n_chunks if self.execute_in_parallel_on_Y else self.X_n_chunks,
self.effective_n_threads,
)
@final
cdef void _parallel_on_X(self) nogil:
"""Perform computation and reduction in parallel on chunks of X.
This strategy dispatches tasks statically on threads. Each task
processes exactly only one chunk of X, computing and reducing
distances matrices between vectors of this chunk and vectors of all
chunks of Y, one chunk of Y at a time.
This strategy is embarrassingly parallel with no intermediate data
structures synchronization at all.
Private datastructures are modified internally by threads.
Private template methods can be implemented on subclasses to
interact with those datastructures at various stages.
"""
cdef:
ITYPE_t Y_start, Y_end, X_start, X_end, X_chunk_idx, Y_chunk_idx
ITYPE_t thread_num
with nogil, parallel(num_threads=self.chunks_n_threads):
thread_num = _openmp_thread_num()
# Allocating thread datastructures
self._parallel_on_X_parallel_init(thread_num)
for X_chunk_idx in prange(self.X_n_chunks, schedule='static'):
X_start = X_chunk_idx * self.X_n_samples_chunk
if X_chunk_idx == self.X_n_chunks - 1:
X_end = X_start + self.X_n_samples_last_chunk
else:
X_end = X_start + self.X_n_samples_chunk
# Reinitializing thread datastructures for the new X chunk
self._parallel_on_X_init_chunk(thread_num, X_start, X_end)
for Y_chunk_idx in range(self.Y_n_chunks):
Y_start = Y_chunk_idx * self.Y_n_samples_chunk
if Y_chunk_idx == self.Y_n_chunks - 1:
Y_end = Y_start + self.Y_n_samples_last_chunk
else:
Y_end = Y_start + self.Y_n_samples_chunk
self._parallel_on_X_pre_compute_and_reduce_distances_on_chunks(
X_start, X_end,
Y_start, Y_end,
thread_num,
)
self._compute_and_reduce_distances_on_chunks(
X_start, X_end,
Y_start, Y_end,
thread_num,
)
# Adjusting thread datastructures on the full pass on Y
self._parallel_on_X_prange_iter_finalize(thread_num, X_start, X_end)
# end: for X_chunk_idx
# Deallocating thread datastructures
self._parallel_on_X_parallel_finalize(thread_num)
# end: with nogil, parallel
return
@final
cdef void _parallel_on_Y(self) nogil:
"""Perform computation and reduction in parallel on chunks of Y.
This strategy is a sequence of embarrassingly parallel subtasks:
chunks of X are iterated over sequentially, and for each chunk of X,
tasks are dispatched statically on threads. Each task processes one
and only one chunk of Y, computing and reducing distances matrices
between vectors of the chunk of X and vectors of the Y.
It comes with lock-free and parallelized intermediate data structures
that synchronize at each iteration of the sequential outer loop on X
chunks.
Private datastructures are modified internally by threads.
Private template methods can be implemented on subclasses to
interact with those datastructures at various stages.
"""
cdef:
ITYPE_t Y_start, Y_end, X_start, X_end, X_chunk_idx, Y_chunk_idx
ITYPE_t thread_num
# Allocating datastructures shared by all threads
self._parallel_on_Y_init()
for X_chunk_idx in range(self.X_n_chunks):
X_start = X_chunk_idx * self.X_n_samples_chunk
if X_chunk_idx == self.X_n_chunks - 1:
X_end = X_start + self.X_n_samples_last_chunk
else:
X_end = X_start + self.X_n_samples_chunk
with nogil, parallel(num_threads=self.chunks_n_threads):
thread_num = _openmp_thread_num()
# Initializing datastructures used in this thread
self._parallel_on_Y_parallel_init(thread_num, X_start, X_end)
for Y_chunk_idx in prange(self.Y_n_chunks, schedule='static'):
Y_start = Y_chunk_idx * self.Y_n_samples_chunk
if Y_chunk_idx == self.Y_n_chunks - 1:
Y_end = Y_start + self.Y_n_samples_last_chunk
else:
Y_end = Y_start + self.Y_n_samples_chunk
self._parallel_on_Y_pre_compute_and_reduce_distances_on_chunks(
X_start, X_end,
Y_start, Y_end,
thread_num,
)
self._compute_and_reduce_distances_on_chunks(
X_start, X_end,
Y_start, Y_end,
thread_num,
)
# end: prange
# end: with nogil, parallel
# Synchronizing the thread datastructures with the main ones
self._parallel_on_Y_synchronize(X_start, X_end)
# end: for X_chunk_idx
# Deallocating temporary datastructures and adjusting main datastructures
self._parallel_on_Y_finalize()
return
# Placeholder methods which have to be implemented
cdef void _compute_and_reduce_distances_on_chunks(
self,
ITYPE_t X_start,
ITYPE_t X_end,
ITYPE_t Y_start,
ITYPE_t Y_end,
ITYPE_t thread_num,
) nogil:
"""Compute the pairwise distances on two chunks of X and Y and reduce them.
This is THE core computational method of BaseDistancesReduction{{name_suffix}}.
This must be implemented in subclasses agnostically from the parallelization
strategies.
"""
return
def _finalize_results(self, bint return_distance):
"""Callback adapting datastructures before returning results.
This must be implemented in subclasses.
"""
return None
# Placeholder methods which can be implemented
cdef void compute_exact_distances(self) nogil:
"""Convert rank-preserving distances to exact distances or recompute them."""
return
cdef void _parallel_on_X_parallel_init(
self,
ITYPE_t thread_num,
) nogil:
"""Allocate datastructures used in a thread given its number."""
return
cdef void _parallel_on_X_init_chunk(
self,
ITYPE_t thread_num,
ITYPE_t X_start,
ITYPE_t X_end,
) nogil:
"""Initialize datastructures used in a thread given its number.
In this method, EuclideanDistance specialisations of subclass of
BaseDistancesReduction _must_ call:
self.middle_term_computer._parallel_on_X_init_chunk(
thread_num, X_start, X_end,
)
to ensure the proper upcast of X[X_start:X_end] to float64 prior
to the reduction with float64 accumulator buffers when X.dtype is
float32.
"""
return
cdef void _parallel_on_X_pre_compute_and_reduce_distances_on_chunks(
self,
ITYPE_t X_start,
ITYPE_t X_end,
ITYPE_t Y_start,
ITYPE_t Y_end,
ITYPE_t thread_num,
) nogil:
"""Initialize datastructures just before the _compute_and_reduce_distances_on_chunks.
In this method, EuclideanDistance specialisations of subclass of
BaseDistancesReduction _must_ call:
self.middle_term_computer._parallel_on_X_pre_compute_and_reduce_distances_on_chunks(
X_start, X_end, Y_start, Y_end, thread_num,
)
to ensure the proper upcast of Y[Y_start:Y_end] to float64 prior
to the reduction with float64 accumulator buffers when Y.dtype is
float32.
"""
return
cdef void _parallel_on_X_prange_iter_finalize(
self,
ITYPE_t thread_num,
ITYPE_t X_start,
ITYPE_t X_end,
) nogil:
"""Interact with datastructures after a reduction on chunks."""
return
cdef void _parallel_on_X_parallel_finalize(
self,
ITYPE_t thread_num
) nogil:
"""Interact with datastructures after executing all the reductions."""
return
cdef void _parallel_on_Y_init(
self,
) nogil:
"""Allocate datastructures used in all threads."""
return
cdef void _parallel_on_Y_parallel_init(
self,
ITYPE_t thread_num,
ITYPE_t X_start,
ITYPE_t X_end,
) nogil:
"""Initialize datastructures used in a thread given its number.
In this method, EuclideanDistance specialisations of subclass of
BaseDistancesReduction _must_ call:
self.middle_term_computer._parallel_on_Y_parallel_init(
thread_num, X_start, X_end,
)
to ensure the proper upcast of X[X_start:X_end] to float64 prior
to the reduction with float64 accumulator buffers when X.dtype is
float32.
"""
return
cdef void _parallel_on_Y_pre_compute_and_reduce_distances_on_chunks(
self,
ITYPE_t X_start,
ITYPE_t X_end,
ITYPE_t Y_start,
ITYPE_t Y_end,
ITYPE_t thread_num,
) nogil:
"""Initialize datastructures just before the _compute_and_reduce_distances_on_chunks.
In this method, EuclideanDistance specialisations of subclass of
BaseDistancesReduction _must_ call:
self.middle_term_computer._parallel_on_Y_pre_compute_and_reduce_distances_on_chunks(
X_start, X_end, Y_start, Y_end, thread_num,
)
to ensure the proper upcast of Y[Y_start:Y_end] to float64 prior
to the reduction with float64 accumulator buffers when Y.dtype is
float32.
"""
return
cdef void _parallel_on_Y_synchronize(
self,
ITYPE_t X_start,
ITYPE_t X_end,
) nogil:
"""Update thread datastructures before leaving a parallel region."""
return
cdef void _parallel_on_Y_finalize(
self,
) nogil:
"""Update datastructures after executing all the reductions."""
return
{{endfor}}
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