def __setitem__(self, key, value):
assert isinstance(value, ndarray.ndarray), "assigned array has to be a pyDive ndarray"
if key == slice(None):
key = [sliceNone] * len(self.shape)
# singe data access is not allowed
assert not all(type(key_comp) is int for key_comp in key),\
"single data access is not allowed"
if not isinstance(key, list) and not isinstance(key, tuple):
key = (key,)
assert len(key) == len(self.shape)
new_shape, clean_slices = helper.subWindow_of_shape(self.shape, key)
assert new_shape == value.shape
# create local slice objects for each engine
local_slices = helper.createLocalSlices(clean_slices, value.distaxis, value.idx_ranges)
# scatter slice objects to the engines
view = com.getView()
view.scatter('window', local_slices, targets=value.targets_in_use)
# write 'value' to disk in parallel
view.execute('%s[tuple(window[0])] = %s' % (self.dataset_name, repr(value)), \
targets=value.targets_in_use)
def __repr__(self):
# if arrays are distributed create a local representation of this object on engine
if onTarget == 'False' and not self.has_local_instance and hasattr(
self.firstArray, "target_ranks"):
items = [item for item in treeItems(self.structOfArrays)]
assert all(self.firstArray.is_distributed_like(a) for name, a in items),\
"Cannot create a local virtual array-of-structs because not all arrays are distributed equally."
self.distaxes = self.firstArray.distaxes
self.target_offsets = self.firstArray.target_offsets
self.target_ranks = self.firstArray.target_ranks
view = com.getView()
self.view = view
# generate a unique variable name used on target representing this instance
global arrayOfStructs_id
self.name = 'arrayOfStructsObj' + str(arrayOfStructs_id)
arrayOfStructs_id += 1
# create a VirtualArrayOfStructs object containing the local arrays on the targets in use
names_tree = makeTree_fromTree(self.structOfArrays,
lambda a: repr(a))
view.push({'names_tree': names_tree}, targets=self.target_ranks)
view.execute('''\
structOfArrays = structured.makeTree_fromTree(names_tree, lambda a_name: globals()[a_name])
%s = structured.structured(structOfArrays)''' % self.name,\
targets=self.target_ranks)
self.has_local_instance = True
return self.name
def __getitem__(self, args):
if args == slice(None):
args = (slice(None) for i in range(len(self.shape)))
if not isinstance(args, list) and not isinstance(args, tuple):
args = [args]
assert len(self.shape) == len(args)
# single data access is not allowed
assert not all(type(arg) is int for arg in args),\
"single data access is not allowed"
new_shape, clean_slices = helper.subWindow_of_shape(self.shape, args)
print "new_shape: ", new_shape
print "clean_slices: ", clean_slices
# result ndarray
result = ndarray_factories.hollow(new_shape, self.distaxis, dtype=self.dtype)
print "result.idx_ranges: ", result.idx_ranges
# create local slice objects for each engine
local_slices = helper.createLocalSlices(clean_slices, self.distaxis, result.idx_ranges)
print "local_slices: ", local_slices
# scatter slice objects to the engines
view = com.getView()
view.scatter('window', local_slices, targets=result.targets_in_use)
view.execute('%s = %s[tuple(window[0])]' % (result.name, self.dataset_name), targets=result.targets_in_use)
return result
def binary_rop(rhs, lhs, op):
lhs = __prepare_operand(lhs, rhs)
result = ndarray_factories.hollow_like(rhs)
view = com.getView()
view.execute("%s = %s %s %s" % (repr(result), repr(lhs), op, repr(rhs)), targets=result.targets_in_use)
return result
def __repr__(self):
# if arrays are distributed create a local representation of this object on engine
if onTarget == 'False' and not self.has_local_instance and hasattr(self.firstArray, "target_ranks"):
items = [item for item in treeItems(self.structOfArrays)]
assert all(self.firstArray.is_distributed_like(a) for name, a in items),\
"Cannot create a local virtual array-of-structs because not all arrays are distributed equally."
self.distaxes = self.firstArray.distaxes
self.target_offsets = self.firstArray.target_offsets
self.target_ranks = self.firstArray.target_ranks
view = com.getView()
self.view = view
# generate a unique variable name used on target representing this instance
global arrayOfStructs_id
self.name = 'arrayOfStructsObj' + str(arrayOfStructs_id)
arrayOfStructs_id += 1
# create a VirtualArrayOfStructs object containing the local arrays on the targets in use
names_tree = makeTree_fromTree(self.structOfArrays, lambda a: repr(a))
view.push({'names_tree' : names_tree}, targets=self.target_ranks)
view.execute('''\
structOfArrays = structured.makeTree_fromTree(names_tree, lambda a_name: globals()[a_name])
%s = structured.structured(structOfArrays)''' % self.name,\
targets=self.target_ranks)
self.has_local_instance = True
return self.name
def n_ary_fun(fun, *args):
a = args[0]
args = [a.name] + [__prepare_operand(arg, a) for arg in args[1:]]
args_str = ", ".join(args)
result = ndarray_factories.hollow_like(a)
view = com.getView()
view.execute("%s = %s(%s)" % (repr(result), fun, args_str), targets=result.targets_in_use)
#\todo: determine dtype from the result of fun and not from args[0]
return result
def __init__(self, shape, distaxis, dtype=np.float, idx_ranges=None, targets_in_use=None, no_allocation=False):
self.shape = list(shape)
self.dtype = dtype
self.distaxis = distaxis
self.view = com.getView()
assert distaxis >= 0 and distaxis < len(self.shape)
if idx_ranges is None and targets_in_use is None:
# number of available targets (engines)
num_targets_av = len(self.view.targets)
# shape of the mpi-local ndarray
localshape = np.array(self.shape)
localshape[distaxis] = (self.shape[distaxis] - 1) / num_targets_av + 1
tmp = localshape[distaxis]
# number of occupied targets by this ndarray instance
num_targets = (self.shape[distaxis] - 1) / localshape[distaxis] + 1
# list of pairs on which each pair stores the range of indices [begin, end) for the distributed axis on each target
# this is the decomposition of the distributed axis
self.idx_ranges = [(r * tmp, (r+1) * tmp) for r in range(0, num_targets-1)]
self.idx_ranges += [((num_targets-1) * tmp, self.shape[distaxis])]
# list of indices of the occupied targets
self.targets_in_use = list(range(num_targets))
elif idx_ranges is not None and targets_in_use is not None:
self.idx_ranges = idx_ranges[:]
self.targets_in_use = targets_in_use[:]
else:
raise ValueError("either args 'idx_ranges' and 'targets_in_use' have to be given both or not given both.")
# generate a unique variable name used on the target representing this instance
global ndarray_id
self.name = 'dist_ndarray' + str(ndarray_id)
ndarray_id += 1
if no_allocation:
self.view.push({self.name : None}, targets=self.targets_in_use)
else:
# instanciate an empty ndarray object of the appropriate shape on each target in use
localshapes = [self.shape[:] for i in range(len(self.targets_in_use))]
for i in range(len(self.targets_in_use)):
localshapes[i][distaxis] = self.idx_ranges[i][1] - self.idx_ranges[i][0]
self.view.scatter('localshape', localshapes, targets=self.targets_in_use)
self.view.push({'dtype' : dtype}, targets=self.targets_in_use)
self.view.execute('%s = empty(localshape[0], dtype=dtype)' % self.name, targets=self.targets_in_use)
def array(array_like, distaxis):
# numpy array
if isinstance(array_like, np.ndarray):
# result ndarray
result = ndarray.ndarray(array_like.shape, distaxis, array_like.dtype, no_allocation=True)
tmp = np.rollaxis(array_like, distaxis)
sub_arrays = [tmp[begin:end] for begin, end in result.idx_ranges]
# roll axis back
sub_arrays = [np.rollaxis(ar, 0, distaxis+1) for ar in sub_arrays]
view = com.getView()
view.scatter('sub_array', sub_arrays, targets=result.targets_in_use)
view.execute("%s = sub_array[0].copy()" % result.name, targets=result.targets_in_use)
return result
def reduce(array, op):
"""Perform a tree-like reduction over all axes of *array*.
:param array: *pyDive.ndarray*, *pyDive.h5_ndarray* or *pyDive.cloned_ndarray* to be reduced
:param numpy-ufunc op: reduce operation, e.g. *numpy.add*.
If the hdf5 data exceeds the memory limit (currently 25% of the combined main memory of all cluster nodes)\
the data will be read block-wise so that a block fits into memory.
"""
def reduce_wrapper(array_name, op_name):
array = globals()[array_name]
op = eval("np." + op_name)
return algorithm.__tree_reduce(array, axis=None, op=op) # reduction over all axes
view = com.getView()
tmp_targets = view.targets # save current target list
if type(array) == VirtualArrayOfStructs:
view.targets = array.firstArray.target_ranks
else:
view.targets = array.target_ranks
result = None
if (hasattr(array, "arraytype") and array.arraytype in hdd_arraytypes) or type(array) in hdd_arraytypes:
for chunk in fragment(array):
array_name = repr(chunk)
targets_results = view.apply(interactive(reduce_wrapper), array_name, op.__name__)
chunk_result = op.reduce(targets_results) # reduce over targets' results
if result is None:
result = chunk_result
else:
result = op(result, chunk_result)
else:
array_name = repr(array)
targets_results = view.apply(interactive(reduce_wrapper), array_name, op.__name__)
result = op.reduce(targets_results) # reduce over targets' results
view.targets = tmp_targets # restore target list
return result
def __bestStepSize(arrays, axis, memory_limit):
view = com.getView()
# minimum amount of memory available and memory needed, both per engine
get_mem_av_node = interactive(lambda: psutil.virtual_memory().available)
tmp_targets = view.targets
view.targets = 'all'
mem_av = min(view.apply(get_mem_av_node)) / com.getPPN()
mem_needed = sum(a.nbytes for a in arrays) / len(view)
view.targets = tmp_targets
# edge length of the whole array
edge_length = arrays[0].shape[axis]
# maximum edge length on one engine according to the available memory
step_size = memory_limit * edge_length * mem_av / mem_needed
if step_size >= edge_length:
return edge_length
# round 'step_size' down to nearest power of two
return pow(2, int(math.log(step_size, 2)))
def __bestStepSize(arrays, axis, memory_limit):
view = com.getView()
# minimum amount of memory available and memory needed, both per engine
get_mem_av_node = interactive(lambda: psutil.virtual_memory().available)
tmp_targets = view.targets
view.targets = 'all'
mem_av = min(view.apply(get_mem_av_node)) / com.getPPN()
mem_needed = sum(a.nbytes for a in arrays) / len(view)
view.targets = tmp_targets
# edge length of the whole array
edge_length = arrays[0].shape[axis]
# maximum edge length on one engine according to the available memory
step_size = memory_limit * edge_length * mem_av / mem_needed
if step_size >= edge_length:
return edge_length
# round 'step_size' down to nearest power of two
return pow(2, int(math.log(step_size, 2)))
def __init__(self, h5_filename, dataset_path, distaxis, max_elements_node=0):
self.h5_filename = h5_filename
self.dataset_path = dataset_path
self.dataset = h5.File(h5_filename, 'r')[dataset_path]
self.shape = list(self.dataset.shape)
self.distaxis = distaxis
self.max_elements_node = max_elements_node
self.dtype = self.dataset.dtype
# generate a unique variable name used on the target representing this instance
global h5_ndarray_id
self.name = 'h5_ndarray' + str(h5_ndarray_id)
h5_ndarray_id += 1
# create dataset object on each target
self.dataset_name = self.name + "_dataset"
self.fileHandle_name = self.name + "_file"
view = com.getView()
view.execute("%s = h5.File('%s', 'r', driver='mpio', comm=MPI.COMM_WORLD)"\
% (self.fileHandle_name, h5_filename))
view.execute("%s = %s['%s']"\
% (self.dataset_name, self.fileHandle_name, dataset_path))
def mapReduce(map_func, reduce_op, *arrays, **kwargs):
"""Applies *map_func* on :term:`engine` on local arrays related to *arrays*
and reduces its result in a tree-like fashion over all axes.
Example: ::
cluster_array = pyDive.ones(shape=[100], distaxes=0)
s = pyDive.mapReduce(lambda a: a**2, np.add, cluster_array) # a is the local numpy-array of *cluster_array*
assert s == 100
:param callable f: function to be called on :term:`engine`. Has to accept *numpy-arrays* and *kwargs*
:param numpy-ufunc reduce_op: reduce operation, e.g. *numpy.add*.
:param arrays: list of arrays including *pyDive.ndarrays*, *pyDive.h5_ndarrays* or *pyDive.cloned_ndarrays*
:param kwargs: user-specified keyword arguments passed to *f*
:raises AssertionError: if the *shapes* of *pyDive.ndarrays* and *pyDive.h5_ndarrays* do not match
:raises AssertionError: if the *distaxes* attributes of *pyDive.ndarrays* and *pyDive.h5_ndarrays* do not match
Notes:
- If the hdf5 data exceeds the memory limit (currently 25% of the combined main memory of all cluster nodes)\
the data will be read block-wise so that a block fits into memory.
- *mapReduce* chooses the list of *engines* from the **first** element of *arrays*. On these engines the mapReduce will be executed.\
If the first array is a *pyDive.h5_ndarray* all engines will be used.
- *mapReduce* is not writing data back to a *pyDive.h5_ndarray* yet.
- *mapReduce* does not equalize the element distribution of *pyDive.ndarrays* before execution.
"""
def mapReduce_wrapper(map_func, reduce_op_name, array_names, **kwargs):
arrays = [globals()[array_name] for array_name in array_names]
reduce_op = eval("np." + reduce_op_name)
return algorithm.__tree_reduce(map_func(*arrays, **kwargs), axis=None, op=reduce_op)
view = com.getView()
tmp_targets = view.targets # save current target list
if type(arrays[0]) == VirtualArrayOfStructs:
view.targets = arrays[0].firstArray.target_ranks
else:
view.targets = arrays[0].target_ranks
result = None
hdd_arrays = [a for a in arrays if (hasattr(a, "arraytype") and a.arraytype in hdd_arraytypes) or type(a) in hdd_arraytypes]
if hdd_arrays:
cloned_arrays = [a for a in arrays if (hasattr(a, "arraytype") and a.arraytype is cloned_ndarray) or type(a) is cloned_ndarray]
other_arrays = [a for a in arrays if not ((hasattr(a, "arraytype") and a.arraytype is cloned_ndarray) or type(a) is cloned_ndarray)]
cloned_arrays_ids = [id(a) for a in cloned_arrays]
other_arrays_ids = [id(a) for a in other_arrays]
for fragments in fragment(*other_arrays):
it_other_arrays = iter(other_arrays)
it_cloned_arrays = iter(cloned_arrays)
array_names = []
for a in arrays:
if id(a) in cloned_arrays_ids:
array_names.append(repr(it_cloned_arrays.next()))
continue
if id(a) in other_arrays_ids:
array_names.append(repr(it_other_arrays.next()))
continue
targets_results = view.apply(interactive(mapReduce_wrapper),\
interactive(map_func), reduce_op.__name__, array_names, **kwargs)
fragment_result = reduce_op.reduce(targets_results) # reduce over targets' results
if result is None:
result = fragment_result
else:
result = reduce_op(result, fragment_result)
else:
array_names = [repr(a) for a in arrays]
targets_results = view.apply(interactive(mapReduce_wrapper),\
interactive(map_func), reduce_op.__name__, array_names, **kwargs)
result = reduce_op.reduce(targets_results) # reduce over targets' results
view.targets = tmp_targets # restore target list
return result
def map(f, *arrays, **kwargs):
"""Applies *f* on :term:`engine` on local arrays related to *arrays*.
Example: ::
cluster_array = pyDive.ones(shape=[100], distaxes=0)
cluster_array *= 2.0
# equivalent to
pyDive.map(lambda a: a *= 2.0, cluster_array) # a is the local numpy-array of *cluster_array*
Or, as a decorator: ::
@pyDive.map
def twice(a):
a *= 2.0
twice(cluster_array)
:param callable f: function to be called on :term:`engine`. Has to accept *numpy-arrays* and *kwargs*
:param arrays: list of arrays including *pyDive.ndarrays*, *pyDive.h5_ndarrays* or *pyDive.cloned_ndarrays*
:param kwargs: user-specified keyword arguments passed to *f*
:raises AssertionError: if the *shapes* of *pyDive.ndarrays* and *pyDive.h5_ndarrays* do not match
:raises AssertionError: if the *distaxes* attributes of *pyDive.ndarrays* and *pyDive.h5_ndarrays* do not match
Notes:
- If the hdf5 data exceeds the memory limit (currently 25% of the combined main memory of all cluster nodes)\
the data will be read block-wise so that a block fits into memory.
- *map* chooses the list of *engines* from the **first** element of *arrays*. On these engines *f* is called.\
If the first array is a *pyDive.h5_ndarray* all engines will be used.
- *map* is not writing data back to a *pyDive.h5_ndarray* yet.
- *map* does not equalize the element distribution of *pyDive.ndarrays* before execution.
"""
if not arrays:
# decorator mode
def map_deco(*arrays, **kwargs):
map(f, *arrays, **kwargs)
return map_deco
def map_wrapper(f, array_names, **kwargs):
arrays = [globals()[array_name] for array_name in array_names]
f(*arrays, **kwargs)
view = com.getView()
tmp_targets = view.targets # save current target list
if type(arrays[0]) == VirtualArrayOfStructs:
view.targets = arrays[0].firstArray.target_ranks
else:
view.targets = arrays[0].target_ranks
hdd_arrays = [a for a in arrays if (hasattr(a, "arraytype") and a.arraytype in hdd_arraytypes) or type(a) in hdd_arraytypes]
if hdd_arrays:
cloned_arrays = [a for a in arrays if (hasattr(a, "arraytype") and a.arraytype is cloned_ndarray) or type(a) is cloned_ndarray]
other_arrays = [a for a in arrays if not ((hasattr(a, "arraytype") and a.arraytype is cloned_ndarray) or type(a) is cloned_ndarray)]
cloned_arrays_ids = [id(a) for a in cloned_arrays]
other_arrays_ids = [id(a) for a in other_arrays]
for fragments in fragment(*other_arrays):
it_other_arrays = iter(other_arrays)
it_cloned_arrays = iter(cloned_arrays)
array_names = []
for a in arrays:
if id(a) in cloned_arrays_ids:
array_names.append(repr(it_cloned_arrays.next()))
continue
if id(a) in other_arrays_ids:
array_names.append(repr(it_other_arrays.next()))
continue
view.apply(interactive(map_wrapper), interactive(f), array_names, **kwargs)
else:
array_names = [repr(a) for a in arrays]
view.apply(interactive(map_wrapper), interactive(f), array_names, **kwargs)
view.targets = tmp_targets # restore target list
def __del__(self):
view = com.getView()
view.execute("%s.close()" % self.fileHandle_name)
def unary_op(a, op):
result = ndarray_factories.hollow_like(a)
view = com.getView()
view.execute("%s = %s%s" % (repr(result), op, repr(a)), targets=result.targets_in_use)
return result
def binary_iop(lhs, rhs, iop):
rhs = __prepare_operand(rhs, lhs)
view = com.getView()
view.execute("%s %s %s" % (repr(lhs), iop, repr(rhs)), targets=lhs.targets_in_use)
return lhs