kde_skbuild now works as well

oleksandr-pavlyk · oleksandr-pavlyk · commit 191bd58f6713 · 2022-07-08T15:33:17.000-05:00
diff --git a/kde_setuptools/setup.py b/kde_setuptools/setup.py
@@ -20,7 +20,7 @@
     name="kde_setuptools",
     author="Intel Corporation",
     version="0.0.1",
-    description="An example of data-parallel extensions built with oneAPI",
+    description="An example of data-parallel Python extensions built with setuptools and oneAPI DPC++",
     long_description="""
     Example of using oneAPI to build data-parallel extension using setuptools.
 
diff --git a/kde_setuptools/tests/.gitignore b/kde_setuptools/tests/.gitignore
@@ -0,0 +1,2 @@
+__pycache__
+*~
diff --git a/kde_skbuild/CMakeLists.txt b/kde_skbuild/CMakeLists.txt
@@ -0,0 +1,65 @@
+cmake_minimum_required(VERSION 3.22 FATAL_ERROR)
+
+project(oneapi_kde_skbuild LANGUAGES C CXX)
+
+if (NOT DEFINED DPCTL_MODULE_PATH)
+  if (DEFINED ENV{DPCTL_MODULE_PATH})
+    set(DPCTL_MODULE_PATH $ENV{DPCTL_MODULE_PATH})
+  else ()
+    mesage(FATAL_ERROR "Specify DPCTL_MODULE_PATH, either via cmake or as environment varibale")
+  endif()
+endif()
+
+message(STATUS "${DPCTL_MODULE_PATH}")
+set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${DPCTL_MODULE_PATH})
+find_package(IntelDPCPP REQUIRED)
+
+set(CMAKE_CXX_STANDARD 17)
+set(CMAKE_CXX_STANDARD_REQUIRED True)
+
+
+# Define CMAKE_INSTALL_xxx: LIBDIR, INCLUDEDIR
+include(GNUInstallDirs)
+
+# Fetch pybind11
+include(FetchContent)
+FetchContent_Declare(
+  pybind11
+  URL https://github.com/pybind/pybind11/archive/refs/tags/v2.9.2.tar.gz
+  URL_HASH SHA256=6bd528c4dbe2276635dc787b6b1f2e5316cf6b49ee3e150264e455a0d68d19c1
+)
+FetchContent_MakeAvailable(pybind11)
+
+find_package(PythonExtensions REQUIRED)
+set(CYTHON_FLAGS "-t -w ${CMAKE_SOURCE_DIR}")
+find_package(Cython REQUIRED)
+find_package(Dpctl REQUIRED)
+
+
+# Pybind11 extension module
+set(py_module_name _pybind11_kde)
+pybind11_add_module(${py_module_name}
+    MODULE
+    ${CMAKE_SOURCE_DIR}/src/pybind11_kde.cpp
+)
+message(STATUS "Dpctl_INCLUDE_DIR: ${Dpctl_INCLUDE_DIR}")
+target_include_directories(${py_module_name}
+    PUBLIC ${CMAKE_SOURCE_DIR}/src ${Dpctl_INCLUDE_DIR}
+)
+install(TARGETS ${py_module_name} DESTINATION kde_skbuild)
+
+# Cython extension
+
+
+set(cy_module_name _cython_kde)
+
+# subdirectory must be known for add_cython_target bails out
+add_subdirectory(${CMAKE_SOURCE_DIR}/src)
+add_cython_target(${cy_module_name} ${CMAKE_SOURCE_DIR}/src/_cython_kde.pyx CXX PY3 OUTPUT_VAR _generated_src)
+add_library(${cy_module_name} MODULE ${_generated_src})
+
+target_include_directories(${cy_module_name} PRIVATE ${NumPy_INCLUDE_DIR} ${Dpctl_INCLUDE_DIR} ${CMAKE_SOURCE_DIR}/src)
+python_extension_module(${cy_module_name})
+install(TARGETS ${cy_module_name} LIBRARY DESTINATION kde_skbuild)
+
+set(ignoreMe "${SKBUILD}")
diff --git a/kde_skbuild/README.md b/kde_skbuild/README.md
@@ -0,0 +1,9 @@
+# Building this extension
+
+Assuming `numpy`, `Cython`, `pybind11`, `pytest`, `scikit-build`, `cmake >=3.21`, and `ninja` are installed
+and DCP++ has been activated:
+
+```bash
+CC=icx CXX=icpx  python setup.py develop -G Ninja -- -DDCPTL_MODULE_PATH=$(python -m dpctl --cmakedir)
+pytest -m tests
+```
diff --git a/kde_skbuild/kde_skbuild/__init__.py b/kde_skbuild/kde_skbuild/__init__.py
@@ -0,0 +1,4 @@
+from ._cython_kde import kde_eval as cython_kde_eval
+from ._pybind11_kde import kde_eval as pybind11_kde_eval
+
+__all__ = ["cyton_kde_eval", "pybind11_kde_eval"]
diff --git a/kde_skbuild/setup.py b/kde_skbuild/setup.py
@@ -0,0 +1,16 @@
+from skbuild import setup
+
+setup(
+    name="kde_skbuild",
+    author="Intel Corporation",
+    version="0.0.1",
+    description="An example of data-parallel Python extensions built with scikit-build and oneAPI DPC++",
+    long_description="""
+    Example of using oneAPI to build data-parallel extension using setuptools.
+
+    Part of oneAPI for Scientific Python community virtual poster.
+    Also see README.md
+    """,
+    license="Apache 2.0",
+    packages=["kde_skbuild",]
+)
diff --git a/kde_skbuild/src/CMakeLists.txt b/kde_skbuild/src/CMakeLists.txt
diff --git a/kde_skbuild/src/_cython_kde.pyx b/kde_skbuild/src/_cython_kde.pyx
@@ -0,0 +1 @@
+../../common_ext/cy_kde.pyx
diff --git a/kde_skbuild/src/kde.hpp b/kde_skbuild/src/kde.hpp
@@ -0,0 +1 @@
+../../common_src/kde.hpp
diff --git a/kde_skbuild/src/pybind11_kde.cpp b/kde_skbuild/src/pybind11_kde.cpp
@@ -0,0 +1 @@
+../../common_ext/py_kde.cpp
diff --git a/kde_skbuild/tests/.gitignore b/kde_skbuild/tests/.gitignore
@@ -0,0 +1,2 @@
+__pycache__
+*~
diff --git a/kde_skbuild/tests/test_cy_kde.py b/kde_skbuild/tests/test_cy_kde.py
@@ -0,0 +1,76 @@
+import numpy as np
+import dpctl
+
+from kde_skbuild import cython_kde_eval as kde_eval
+
+import pytest
+
+def ref_kde(x, data, h):
+    """
+    Reference NumPy implementation for KDE evaluation
+    """
+    assert x.ndim == 2 and data.ndim == 2
+    assert x.shape[1] == data.shape[1]
+    dim = x.shape[1]
+    n_data = data.shape[0]
+    return np.exp(
+        np.square(x[:, np.newaxis, :]-data).sum(axis=-1)/(-2*h*h)
+    ).sum(axis=1)/(np.sqrt(2*np.pi)*h)**dim / n_data
+
+
+def test_1d():
+    try:
+        q = dpctl.SyclQueue()
+    except dpctl.SyclQueueCreationError:
+        pytest.skip("Execution queue could not be created, skipping...")
+
+    x = np.linspace(0.1, 0.9, num=15).reshape((-1, 1))
+    data = np.random.rand(128,1)
+
+    f_cy = kde_eval(q, x, data, 0.1)
+    f_ref = ref_kde(x, data, 0.1)
+
+    assert np.allclose(f_cy, f_ref)
+
+
+def test_2d():
+    try:
+        q = dpctl.SyclQueue()
+    except dpctl.SyclQueueCreationError:
+        pytest.skip("Execution queue could not be created, skipping...")
+
+    x = np.dstack(
+        np.meshgrid(
+            np.linspace(0.1, 0.9, num=7),
+            np.linspace(0.1, 0.9, num=7)
+        )
+    ).reshape(-1, 2)
+
+    data = np.random.rand(128*128, 2)
+
+    f_cy = kde_eval(q, x, data, 0.05)
+    f_ref = ref_kde(x, data, 0.05)
+
+    assert np.allclose(f_cy, f_ref)
+
+
+def test_3d():
+    try:
+        q = dpctl.SyclQueue()
+    except dpctl.SyclQueueCreationError:
+        pytest.skip("Execution queue could not be created, skipping...")
+
+    x = np.dstack(
+        np.meshgrid(
+            np.linspace(0.1, 0.9, num=7),
+            np.linspace(0.1, 0.9, num=7),
+            np.linspace(0.1, 0.9, num=7)
+        )
+    ).reshape(-1, 3)
+
+    data = np.random.rand(16000,3)
+
+    f_cy = kde_eval(q, x, data, 0.01)
+    f_ref = ref_kde(x, data, 0.01)
+
+    assert np.allclose(f_cy, f_ref)
diff --git a/kde_skbuild/tests/test_py_kde.py b/kde_skbuild/tests/test_py_kde.py
@@ -0,0 +1,76 @@
+import numpy as np
+import dpctl
+
+from kde_skbuild import pybind11_kde_eval as kde_eval
+
+import pytest
+
+def ref_kde(x, data, h):
+    """
+    Reference NumPy implementation for KDE evaluation
+    """
+    assert x.ndim == 2 and data.ndim == 2
+    assert x.shape[1] == data.shape[1]
+    dim = x.shape[1]
+    n_data = data.shape[0]
+    return np.exp(
+        np.square(x[:, np.newaxis, :]-data).sum(axis=-1)/(-2*h*h)
+    ).sum(axis=1)/(np.sqrt(2*np.pi)*h)**dim / n_data
+
+
+def test_1d():
+    try:
+        q = dpctl.SyclQueue()
+    except dpctl.SyclQueueCreationError:
+        pytest.skip("Execution queue could not be created, skipping...")
+
+    x = np.linspace(0.1, 0.9, num=15).reshape((-1, 1))
+    data = np.random.rand(128,1)
+
+    f_cy = kde_eval(q, x, data, 0.1)
+    f_ref = ref_kde(x, data, 0.1)
+
+    assert np.allclose(f_cy, f_ref)
+
+
+def test_2d():
+    try:
+        q = dpctl.SyclQueue()
+    except dpctl.SyclQueueCreationError:
+        pytest.skip("Execution queue could not be created, skipping...")
+
+    x = np.dstack(
+        np.meshgrid(
+            np.linspace(0.1, 0.9, num=7),
+            np.linspace(0.1, 0.9, num=7)
+        )
+    ).reshape(-1, 2)
+
+    data = np.random.rand(128*128, 2)
+
+    f_cy = kde_eval(q, x, data, 0.05)
+    f_ref = ref_kde(x, data, 0.05)
+
+    assert np.allclose(f_cy, f_ref)
+
+
+def test_3d():
+    try:
+        q = dpctl.SyclQueue()
+    except dpctl.SyclQueueCreationError:
+        pytest.skip("Execution queue could not be created, skipping...")
+
+    x = np.dstack(
+        np.meshgrid(
+            np.linspace(0.1, 0.9, num=7),
+            np.linspace(0.1, 0.9, num=7),
+            np.linspace(0.1, 0.9, num=7)
+        )
+    ).reshape(-1, 3)
+
+    data = np.random.rand(16000,3)
+
+    f_cy = kde_eval(q, x, data, 0.01)
+    f_ref = ref_kde(x, data, 0.01)
+
+    assert np.allclose(f_cy, f_ref)
