File size: 10,094 Bytes
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import numpy as np
cdef class QueryAttr(object):
cdef unicode name
cdef np.dtype dtype
def __init__(self, name, dtype):
self.name = name
self.dtype = dtype
cdef dict execute_multi_index(Array array,
tiledb_query_t* query_ptr,
tuple attr_names,
return_coord):
# NOTE: query_ptr *must* only be freed in caller
cdef:
tiledb_ctx_t* ctx_ptr = <tiledb_ctx_t*>PyCapsule_GetPointer(
array.ctx.__capsule__(), "ctx")
tiledb_query_status_t query_status
cdef:
uint64_t result_bytes = 0
size_t result_elements
float result_elements_f, result_rem
uint64_t el_count = 0
bint repeat_query = True
uint64_t repeat_count = 0
uint64_t buffer_bytes_remaining = 0
uint64_t* buffer_sizes_ptr = NULL
cdef:
np.dtype coords_dtype
cdef:
Py_ssize_t attr_idx
bytes battr_name
unicode attr_name
np.ndarray attr_array
np.dtype attr_dtype
QueryAttr qattr
cdef list attrs = list()
# Coordinate attribute buffers must be set first
if return_coord:
dims = tuple(array.schema.domain.dim(dim_idx) for dim_idx in \
range(array.schema.ndim))
attrs += [QueryAttr(dim.name, dim.dtype) for dim in dims]
# Get the attributes
attrs += [QueryAttr(a.name, a.dtype)
for a in [array.schema.attr(name)
for name in attr_names]]
# Create and assign attribute result buffers
cdef Py_ssize_t nattr = len(attrs)
cdef uint64_t ndim = array.ndim
cdef dict result_dict = dict()
cdef np.ndarray buffer_sizes = np.zeros(nattr, np.uint64)
cdef np.ndarray result_bytes_read = np.zeros(nattr, np.uint64)
cdef uint64_t init_buffer_size = 1310720 * 8 # 10 MB int64
if 'py.init_buffer_bytes' in array.ctx.config():
init_buffer_size = int(array.ctx.config()['py.init_buffer_bytes'])
# switch from exponential to linear (+4GB) allocation
cdef uint64_t linear_alloc_bytes = 4 * (2**30) # 4 GB
# There are two different conditions which may cause incomplete queries,
# requiring retries and potentially reallocation to complete the read.
# 1) user-allocated buffer is not large enough. In this case, we need to
# allocate more memory and retry. This is accomplished below by resizing
# the array in-place (preserving the existing data), then bumping the
# query buffer pointer.
# 2) internal memory limit is exceeded: the libtiledb parameter
# 'sm.memory_budget' governs internal memory allocation. If libtiledb's
# internal allocation exceeds this budget, the query may need to be
# retried, but we do not necessarily need to bump the user buffer allocation.
while repeat_query:
for attr_idx in range(nattr):
qattr = attrs[attr_idx]
attr_name = qattr.name
attr_dtype = qattr.dtype
# allocate initial array
if repeat_count == 0:
result_dict[attr_name] = np.zeros(int(init_buffer_size / attr_dtype.itemsize),
dtype=attr_dtype)
# Get the array here in order to save a lookup
attr_array = result_dict[attr_name]
if repeat_count > 0:
buffer_bytes_remaining = attr_array.nbytes - result_bytes_read[attr_idx]
if buffer_sizes[attr_idx] > (.25 * buffer_bytes_remaining):
# Check number of bytes read during the *last* pass.
# The conditional above handles situation (2) in order to avoid re-allocation
# on every repeat, in case we are reading small chunks at a time due to libtiledb
# memory budget.
# TODO make sure 'refcheck=False' is always safe
if attr_array.nbytes < linear_alloc_bytes:
attr_array.resize(attr_array.size * 2, refcheck=False)
else:
new_size = attr_array.size + linear_alloc_bytes / attr_dtype.itemsize
attr_array.resize(new_size, refcheck=False)
battr_name = attr_name.encode('UTF-8')
attr_array_ptr = np.PyArray_DATA(attr_array)
# we need to give the pointer to the current starting point after reallocation
attr_array_ptr = \
<void*>(<char*>attr_array_ptr + <ptrdiff_t>result_bytes_read[attr_idx])
buffer_sizes[attr_idx] = attr_array.nbytes - result_bytes_read[attr_idx]
buffer_sizes_ptr = <uint64_t*>np.PyArray_DATA(buffer_sizes)
rc = tiledb_query_set_data_buffer(
ctx_ptr, query_ptr, battr_name, attr_array_ptr,
&(buffer_sizes_ptr[attr_idx]))
if rc != TILEDB_OK:
# NOTE: query_ptr *must* only be freed in caller
_raise_ctx_err(ctx_ptr, rc)
with nogil:
rc = tiledb_query_submit(ctx_ptr, query_ptr)
if rc != TILEDB_OK:
# NOTE: query_ptr *must* only be freed in caller
_raise_ctx_err(ctx_ptr, rc)
# update bytes-read count
for attr_idx in range(nattr):
result_bytes_read[attr_idx] += buffer_sizes[attr_idx]
rc = tiledb_query_get_status(ctx_ptr, query_ptr, &query_status)
if rc != TILEDB_OK:
# NOTE: query_ptr *must* only be freed in caller
_raise_ctx_err(ctx_ptr, rc)
if query_status == TILEDB_INCOMPLETE:
#printf("%s\n", <const char*>"got incomplete!")
repeat_query = True
repeat_count += 1
elif query_status == TILEDB_COMPLETED:
repeat_query = False
break
elif query_status == TILEDB_FAILED:
raise TileDBError("Query returned TILEDB_FAILED")
elif query_status == TILEDB_INPROGRESS:
raise TileDBError("Query returned TILEDB_INPROGRESS")
elif query_status == TILEDB_INCOMPLETE:
raise TileDBError("Query returned TILEDB_INCOMPLETE")
else:
raise TileDBError("internal error: unknown query status")
# resize arrays to final bytes-read
for attr_idx in range(nattr):
qattr = attrs[attr_idx]
attr_name = qattr.name
attr_dtype = qattr.dtype
attr_item_size = attr_dtype.itemsize
attr_array = result_dict[attr_name]
attr_array.resize(int(result_bytes_read[attr_idx] / attr_item_size), refcheck=False)
return result_dict
cpdef multi_index(Array array, tuple attr_names, tuple ranges,
order = None, coords = None):
cdef tiledb_layout_t layout = TILEDB_UNORDERED
if order is None or order == 'C':
layout = TILEDB_ROW_MAJOR
elif order == 'F':
layout = TILEDB_COL_MAJOR
elif order == 'G':
layout = TILEDB_GLOBAL_ORDER
else:
raise ValueError("order must be 'C' (TILEDB_ROW_MAJOR), "\
"'F' (TILEDB_COL_MAJOR), "\
"or 'G' (TILEDB_GLOBAL_ORDER)")
cdef tiledb_ctx_t* ctx_ptr = <tiledb_ctx_t*>PyCapsule_GetPointer(
array.ctx.__capsule__(), "ctx")
cdef tiledb_array_t* array_ptr = array.ptr
cdef tiledb_query_t* query_ptr = NULL
cdef int rc = TILEDB_OK
rc = tiledb_query_alloc(ctx_ptr, array_ptr, TILEDB_READ, &query_ptr)
if rc != TILEDB_OK:
tiledb_query_free(&query_ptr)
_raise_ctx_err(ctx_ptr, rc)
rc = tiledb_query_set_layout(ctx_ptr, query_ptr, layout)
if rc != TILEDB_OK:
tiledb_query_free(&query_ptr)
_raise_ctx_err(ctx_ptr, rc)
dim = array.schema.domain.dim(0)
cdef uint32_t c_dim_idx
cdef void* start_ptr = NULL
cdef void* end_ptr = NULL
cdef tuple cur_range
cdef np.ndarray start
cdef np.ndarray end
# Add ranges to query
#####################
# we loop over the range tuple left to right and apply
# (unspecified dimensions are excluded)
cdef Py_ssize_t dim_idx, range_idx
cdef tiledb_subarray_t* subarray_ptr = NULL
cdef bint is_default = True
rc = tiledb_subarray_alloc(ctx_ptr, array_ptr, &subarray_ptr)
if rc != TILEDB_OK:
tiledb_subarray_free(&subarray_ptr)
tiledb_query_free(&query_ptr)
_raise_ctx_err(ctx_ptr, rc)
for dim_idx in range(len(ranges)):
c_dim_idx = <uint32_t>dim_idx
dim_ranges = ranges[dim_idx]
# skip empty dimensions
if len(dim_ranges) == 0:
continue
is_default = False
for range_idx in range(len(dim_ranges)):
if len(dim_ranges[range_idx]) != 2:
tiledb_subarray_free(&subarray_ptr)
tiledb_query_free(&query_ptr)
raise TileDBError("internal error: invalid sub-range: ", dim_ranges[range_idx])
start = np.array(dim_ranges[range_idx][0], dtype=dim.dtype)
end = np.array(dim_ranges[range_idx][1], dtype=dim.dtype)
start_ptr = np.PyArray_DATA(start)
end_ptr = np.PyArray_DATA(end)
rc = tiledb_subarray_add_range(
ctx_ptr, subarray_ptr, dim_idx, start_ptr, end_ptr, NULL)
if rc != TILEDB_OK:
tiledb_subarray_free(&subarray_ptr)
tiledb_query_free(&query_ptr)
_raise_ctx_err(ctx_ptr, rc)
if not is_default:
rc = tiledb_query_set_subarray_t(ctx_ptr, query_ptr, subarray_ptr)
if rc != TILEDB_OK:
tiledb_subarray_free(&subarray_ptr)
tiledb_query_free(&query_ptr)
_raise_ctx_err(ctx_ptr, rc)
try:
if coords is None:
coords = True
result = execute_multi_index(array, query_ptr, attr_names, coords)
finally:
tiledb_query_free(&query_ptr)
return result
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