From 8e4f11368f12839369fc032f0e3ab9c0262fb6d4 Mon Sep 17 00:00:00 2001
From: JM Etancelin <jean-matthieu.etancelin@univ-pau.fr>
Date: Wed, 17 Mar 2021 16:41:04 +0100
Subject: [PATCH] fix numpy deprecation and allocation alignment
---
hysop/backend/host/host_buffer.py | 29 +++++++++++++++++------------
hysop/core/memory/allocator.py | 25 +++++++++++++------------
2 files changed, 30 insertions(+), 24 deletions(-)
diff --git a/hysop/backend/host/host_buffer.py b/hysop/backend/host/host_buffer.py
index 9d343d21b..7e44b22ba 100644
--- a/hysop/backend/host/host_buffer.py
+++ b/hysop/backend/host/host_buffer.py
@@ -1,9 +1,11 @@
import numpy as np
+import ctypes as C
from hysop.constants import MemoryOrdering, default_order
from hysop.tools.types import check_instance
from hysop.core.memory.buffer import Buffer, PooledBuffer
+
class HostBuffer(np.ndarray, Buffer):
"""
Host buffer class.
@@ -11,22 +13,22 @@ class HostBuffer(np.ndarray, Buffer):
__array_priority__ = -1.0
def __new__(cls, size,
- shape=None, dtype=np.uint8, order=None,
- buffer=None, offset=0, strides=None):
+ shape=None, dtype=np.uint8, order=None,
+ buffer=None, offset=0, strides=None):
from_buffer = False
if isinstance(buffer, Buffer):
__buffer = buffer
- buffer = buffer.buf
+ buffer = buffer.buf
from_buffer = True
- obj = super(HostBuffer,cls).__new__(cls,
- shape=shape or (size,), dtype=dtype, order=order,
- buffer=buffer, offset=offset, strides=strides)
+ obj = super(HostBuffer, cls).__new__(cls,
+ shape=shape or (size,), dtype=dtype, order=order,
+ buffer=buffer, offset=offset, strides=strides)
- #keep a reference to the buffer (usefull for pooled buffers)
- #such that buffer.__del__ will only be called when all views
- #on this HostBuffer have been destroyed.
+ # keep a reference to the buffer (usefull for pooled buffers)
+ # such that buffer.__del__ will only be called when all views
+ # on this HostBuffer have been destroyed.
if from_buffer and isinstance(__buffer, HostPooledBuffer):
obj._hysop_base_data = __buffer
@@ -38,11 +40,13 @@ class HostBuffer(np.ndarray, Buffer):
def __str__(self):
return self.view(np.ndarray).__str__()
+
def __repr__(self):
return self.view(np.ndarray).__repr__()
def get_int_ptr(self):
return self.ctypes.data
+
def release(self):
pass
@@ -51,7 +55,7 @@ class HostBuffer(np.ndarray, Buffer):
"""
Given int ptr should never be freed, numpy take ownership.
"""
- buf = np.core.multiarray.int_asbuffer(int_ptr_value, size)
+ buf = np.ctypeslib.as_array(C.cast(int_ptr_value, C.POINTER(C.c_uint8)), (size,))
return cls.from_buffer(buf)
@classmethod
@@ -62,7 +66,7 @@ class HostBuffer(np.ndarray, Buffer):
def aligned_view(self, alignment, size=None):
assert self.ndim == 1
assert self.dtype == np.uint8
- assert alignment>0
+ assert alignment > 0
assert not (alignment & (alignment-1)), 'alignment is not a power of 2.'
ptr = self.get_int_ptr()
offset = -ptr % alignment
@@ -70,7 +74,7 @@ class HostBuffer(np.ndarray, Buffer):
size = self.size-offset
else:
assert self.size >= (offset+size)
- buf = self.__getitem__(slice(offset,offset+size))
+ buf = self.__getitem__(slice(offset, offset+size))
return buf
@classmethod
@@ -82,6 +86,7 @@ class HostBuffer(np.ndarray, Buffer):
int_ptr = property(get_int_ptr)
+
class HostPooledBuffer(PooledBuffer):
def get_array(self):
return self._bufview
diff --git a/hysop/core/memory/allocator.py b/hysop/core/memory/allocator.py
index 46616a61f..4f93e42c0 100644
--- a/hysop/core/memory/allocator.py
+++ b/hysop/core/memory/allocator.py
@@ -1,4 +1,3 @@
-
import traceback
from abc import ABCMeta, abstractmethod
from hysop import __VERBOSE__, __TRACE_MEMALLOCS__, __BACKTRACE_BIG_MEMALLOCS__
@@ -7,12 +6,13 @@ from hysop.tools.units import bytes2str
from hysop.tools.types import first_not_None
from hysop.tools.handle import TaggedObject
+
class AllocatorBase(TaggedObject, metaclass=ABCMeta):
"""
Base class for allocators.
"""
- is_deferred=False
+ is_deferred = False
def __new__(cls, verbose, **kwds):
return super(AllocatorBase, cls).__new__(cls, tag_prefix='al', **kwds)
@@ -24,8 +24,10 @@ class AllocatorBase(TaggedObject, metaclass=ABCMeta):
def __eq__(self, other):
return (self is other)
+
def __ne__(self, other):
return (self is not other)
+
def __hash__(self):
return id(self)
@@ -39,12 +41,12 @@ class AllocatorBase(TaggedObject, metaclass=ABCMeta):
try_count = 0
while try_count < 2:
try:
- if (alignment > 1):
- buf = self.allocate_aligned(size=size, alignment=alignment)
- else:
+ if alignment is None or alignment == 1:
buf = self.allocate(nbytes=size)
+ else:
+ buf = self.allocate_aligned(size=size, alignment=alignment)
if (buf is None):
- msg='{}.allocate(): returned allocation is None.'.format(self.__class__)
+ msg = '{}.allocate(): returned allocation is None.'.format(self.__class__)
raise ValueError(msg)
return buf
except MemoryError:
@@ -80,8 +82,8 @@ class AllocatorBase(TaggedObject, metaclass=ABCMeta):
"""
if (self._verbose or __BACKTRACE_BIG_MEMALLOCS__) and verbose:
print('{}allocating block of size {}.'.format(
- self.prefix(), bytes2str(nbytes)))
- if __BACKTRACE_BIG_MEMALLOCS__ and nbytes>64*1024*1024:
+ self.prefix(), bytes2str(nbytes)))
+ if __BACKTRACE_BIG_MEMALLOCS__ and nbytes > 64*1024*1024:
print('[BIG ALLOCATION BACKTRACE]')
print(''.join(traceback.format_stack()))
print('[END OF TRACE]')
@@ -91,12 +93,12 @@ class AllocatorBase(TaggedObject, metaclass=ABCMeta):
"""
Allocate size bytes aligned on alignment.
"""
- assert alignment>0
- assert (alignment & (alignment-1))==0, 'alignment is not a power of 2.'
+ assert alignment > 0
+ assert (alignment & (alignment-1)) == 0, 'alignment is not a power of 2.'
nbytes = size + alignment - 1
if self._verbose:
print('{}allocating block of size {}, to satisfy {} aligned on {} bytes.'.format(
- self.prefix(), bytes2str(nbytes), bytes2str(size), alignment))
+ self.prefix(), bytes2str(nbytes), bytes2str(size), alignment))
return self.allocate(nbytes, verbose=False).aligned_view(alignment=alignment, size=size)
def try_release_blocks(self):
@@ -111,4 +113,3 @@ class AllocatorBase(TaggedObject, metaclass=ABCMeta):
Release the allocated buffer.
"""
buf.release()
-
--
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