Moving TestDeviceBuffer to pylibraft.common.device_ndarray

python/pylibraft/pylibraft/cluster/experimental/CMakeLists.txt

@@ -0,0 +1,28 @@
+# =============================================================================
+# Copyright (c) 2022, NVIDIA CORPORATION.
+#
+# Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except
+# in compliance with the License. You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software distributed under the License
+# is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express
+# or implied. See the License for the specific language governing permissions and limitations under
+# the License.
+# =============================================================================
+
+# Set the list of Cython files to build
+set(cython_sources kmeans.pyx)
+set(linked_libraries raft::raft raft::distance)
+
+# Build all of the Cython targets
+rapids_cython_create_modules(
+  CXX
+  SOURCE_FILES "${cython_sources}"
+  LINKED_LIBRARIES "${linked_libraries}" MODULE_PREFIX cluster_experimental_
+)
+
+foreach(cython_module IN LISTS RAPIDS_CYTHON_CREATED_TARGETS)
+  set_target_properties(${cython_module} PROPERTIES INSTALL_RPATH "\$ORIGIN;\$ORIGIN/../library")
+endforeach()

python/pylibraft/pylibraft/common/__init__.py

@@ -13,5 +13,7 @@
 # limitations under the License.
 #
 
+
 from .cuda import Stream
+from .device_ndarray import device_ndarray
 from .handle import Handle

python/pylibraft/pylibraft/common/device_ndarray.py

@@ -0,0 +1,112 @@
+# Copyright (c) 2022, NVIDIA CORPORATION.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+
+import numpy as np
+
+import rmm
+
+
+class device_ndarray:
+    """
+    raft.device_ndarray is meant to be a very lightweight
+    __cuda_array_interface__ wrapper around a numpy.ndarray.
+    """
+
+    def __init__(self, np_ndarray):
+        """
+        Construct a raft.device_ndarray wrapper around a numpy.ndarray
+
+        Parameters
+        ----------
+        ndarray : A numpy.ndarray which will be copied and moved to the device
+        """
+        self.ndarray_ = np_ndarray
+        order = "C" if self.c_contiguous else "F"
+        self.device_buffer_ = rmm.DeviceBuffer.to_device(
+            self.ndarray_.tobytes(order=order)
+        )
+
+    @property
+    def c_contiguous(self):
+        """
+        Is the current device_ndarray laid out in row-major format?
+        """
+        array_interface = self.ndarray_.__array_interface__
+        strides = self.strides
+        return (
+            strides is None
+            or array_interface["strides"][1] == self.dtype.itemsize
+        )
+
+    @property
+    def f_contiguous(self):
+        """
+        Is the current device_ndarray laid out in column-major format?
+        """
+        return not self.c_contiguous
+
+    @property
+    def dtype(self):
+        """
+        Datatype of the current device_ndarray instance
+        """
+        array_interface = self.ndarray_.__array_interface__
+        return np.dtype(array_interface["typestr"])
+
+    @property
+    def shape(self):
+        """
+        Shape of the current device_ndarray instance
+        """
+        array_interface = self.ndarray_.__array_interface__
+        return array_interface["shape"]
+
+    @property
+    def strides(self):
+        """
+        Strides of the current device_ndarray instance
+        """
+        array_interface = self.ndarray_.__array_interface__
+        return (
+            None
+            if "strides" not in array_interface
+            else array_interface["strides"]
+        )
+
+    @property
+    def __cuda_array_interface__(self):
+        """
+        Returns the __cuda_array_interface__ compliant dict for
+        integrating with other device-enabled libraries using
+        zero-copy semantics.
+        """
+        device_cai = self.device_buffer_.__cuda_array_interface__
+        host_cai = self.ndarray_.__array_interface__.copy()
+        host_cai["data"] = (device_cai["data"][0], device_cai["data"][1])
+
+        return host_cai
+
+    def copy_to_host(self):
+        """
+        Returns a new numpy.ndarray object on host with the current contents of
+        this device_ndarray
+        """
+        ret = np.frombuffer(
+            self.device_buffer_.tobytes(),
+            dtype=self.dtype,
+            like=self.ndarray_,
+        ).astype(self.dtype)
+        ret = np.lib.stride_tricks.as_strided(ret, self.shape, self.strides)
+        return ret

python/pylibraft/pylibraft/distance/pairwise_distance.pyx

@@ -28,8 +28,11 @@ from .distance_type cimport DistanceType
 
 from pylibraft.common import Handle
 from pylibraft.common.handle import auto_sync_handle
+
 from pylibraft.common.handle cimport handle_t
 
+from pylibraft.common import device_ndarray
+
 
 def is_c_cont(cai, dt):
     return "strides" not in cai or \
@@ -92,7 +95,7 @@ SUPPORTED_DISTANCES = ["euclidean", "l1", "cityblock", "l2", "inner_product",
 
 
 @auto_sync_handle
-def distance(X, Y, dists, metric="euclidean", p=2.0, handle=None):
+def distance(X, Y, out=None, metric="euclidean", p=2.0, handle=None):
     """
     Compute pairwise distances between X and Y
 
@@ -107,11 +110,16 @@ def distance(X, Y, dists, metric="euclidean", p=2.0, handle=None):
 
     X : CUDA array interface compliant matrix shape (m, k)
     Y : CUDA array interface compliant matrix shape (n, k)
-    dists : Writable CUDA array interface matrix shape (m, n)
+    out : Optional writable CUDA array interface matrix shape (m, n)
     metric : string denoting the metric type (default="euclidean")
     p : metric parameter (currently used only for "minkowski")
     {handle_docstring}
 
+    Returns
+    -------
+
+    raft.device_ndarray containing pairwise distances
+
     Examples
     --------
 
@@ -144,14 +152,24 @@ def distance(X, Y, dists, metric="euclidean", p=2.0, handle=None):
 
     x_cai = X.__cuda_array_interface__
     y_cai = Y.__cuda_array_interface__
-    dists_cai = dists.__cuda_array_interface__
 
     m = x_cai["shape"][0]
     n = y_cai["shape"][0]
 
+    x_dt = np.dtype(x_cai["typestr"])
+    y_dt = np.dtype(y_cai["typestr"])
+
+    if out is None:
+        out_host = np.empty((m, n), dtype=y_dt)
+        dists = device_ndarray(out_host)
+    else:
+        dists = out
+
     x_k = x_cai["shape"][1]
     y_k = y_cai["shape"][1]
 
+    dists_cai = dists.__cuda_array_interface__
+
     if x_k != y_k:
         raise ValueError("Inputs must have same number of columns. "
                          "a=%s, b=%s" % (x_k, y_k))
@@ -163,8 +181,6 @@ def distance(X, Y, dists, metric="euclidean", p=2.0, handle=None):
     handle = handle if handle is not None else Handle()
     cdef handle_t *h = <handle_t*><size_t>handle.getHandle()
 
-    x_dt = np.dtype(x_cai["typestr"])
-    y_dt = np.dtype(y_cai["typestr"])
     d_dt = np.dtype(dists_cai["typestr"])
 
     x_c_contiguous = is_c_cont(x_cai, x_dt)
@@ -205,3 +221,5 @@ def distance(X, Y, dists, metric="euclidean", p=2.0, handle=None):
                           <float>p)
     else:
         raise ValueError("dtype %s not supported" % x_dt)
+
+    return dists

python/pylibraft/pylibraft/test/test_device_buffer.py

@@ -0,0 +1,42 @@
+# Copyright (c) 2022, NVIDIA CORPORATION.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+
+import numpy as np
+import pytest
+
+from pylibraft.common import device_ndarray
+
+
+@pytest.mark.parametrize("order", ["F", "C"])
+@pytest.mark.parametrize("dtype", [np.float32, np.float64])
+def test_basic_attributes(order, dtype):
+
+    a = np.random.random((500, 2)).astype(dtype)
+
+    if order == "C":
+        a = np.ascontiguousarray(a)
+    else:
+        a = np.asfortranarray(a)
+
+    db = device_ndarray(a)
+    db_host = db.copy_to_host()
+
+    assert a.shape == db.shape
+    assert a.dtype == db.dtype
+    assert a.data.f_contiguous == db.f_contiguous
+    assert a.data.f_contiguous == db_host.data.f_contiguous
+    assert a.data.c_contiguous == db.c_contiguous
+    assert a.data.c_contiguous == db_host.data.c_contiguous
+    np.testing.assert_array_equal(a.tolist(), db_host.tolist())

python/pylibraft/pylibraft/test/test_distance.py

@@ -17,9 +17,8 @@
 import pytest
 from scipy.spatial.distance import cdist
 
-from pylibraft.common import Handle
+from pylibraft.common import Handle, device_ndarray
 from pylibraft.distance import pairwise_distance
-from pylibraft.testing.utils import TestDeviceBuffer
 
 
 @pytest.mark.parametrize("n_rows", [100])
@@ -39,9 +38,10 @@
         "sqeuclidean",
     ],
 )
+@pytest.mark.parametrize("inplace", [True, False])
 @pytest.mark.parametrize("order", ["F", "C"])
 @pytest.mark.parametrize("dtype", [np.float32, np.float64])
-def test_distance(n_rows, n_cols, metric, order, dtype):
+def test_distance(n_rows, n_cols, inplace, metric, order, dtype):
     input1 = np.random.random_sample((n_rows, n_cols))
     input1 = np.asarray(input1, order=order).astype(dtype)
 
@@ -61,13 +61,17 @@ def test_distance(n_rows, n_cols, metric, order, dtype):
 
     expected[expected <= 1e-5] = 0.0
 
-    input1_device = TestDeviceBuffer(input1, order)
-    output_device = TestDeviceBuffer(output, order)
+    input1_device = device_ndarray(input1)
+    output_device = device_ndarray(output) if inplace else None
 
     handle = Handle()
-    pairwise_distance(input1_device, input1_device, output_device, metric)
+    ret_output = pairwise_distance(
+        input1_device, input1_device, output_device, metric
+    )
     handle.sync()
 
+    output_device = ret_output if not inplace else output_device
+
     actual = output_device.copy_to_host()
 
     actual[actual <= 1e-5] = 0.0

python/pylibraft/pylibraft/test/test_fused_l2_argmin.py

@@ -17,9 +17,8 @@
 import pytest
 from scipy.spatial.distance import cdist
 
-from pylibraft.common import Handle
+from pylibraft.common import Handle, device_ndarray
 from pylibraft.distance import fused_l2_nn_argmin
-from pylibraft.testing.utils import TestDeviceBuffer
 
 
 @pytest.mark.parametrize("n_rows", [10, 100])
@@ -38,9 +37,9 @@ def test_fused_l2_nn_minarg(n_rows, n_cols, n_clusters, dtype):
 
     expected = expected.argmin(axis=1)
 
-    input1_device = TestDeviceBuffer(input1, "C")
-    input2_device = TestDeviceBuffer(input2, "C")
-    output_device = TestDeviceBuffer(output, "C")
+    input1_device = device_ndarray(input1)
+    input2_device = device_ndarray(input2)
+    output_device = device_ndarray(output)
 
     handle = Handle()
     fused_l2_nn_argmin(