An example to demonstrate that a very basic functionality works

example/example.py

@@ -0,0 +1,55 @@
+import pyArborX
+
+
+def run():
+    num_points = 100
+
+    radius = 2.0
+
+    # Type alias
+    ExecutionSpace = pyArborX.ExecutionSpace
+    Primitives = pyArborX.Kokkos_View_ArborX_Point_1D_Default
+    Point = pyArborX.Point
+    BVH = pyArborX.BVH
+
+    execution_space = ExecutionSpace()
+
+    primitives = Primitives("primitives", num_points)
+    for i in range(primitives.size()):
+        primitives[i] = Point(i, i, i)
+
+    queries = pyArborX.generateWithinQueries_device(
+        execution_space,
+        primitives,
+        num_points,
+        radius,
+    )
+    #  execution_space.fence()
+
+    bvh = BVH(execution_space, primitives)
+
+    offsets = pyArborX.intView1D("offsets", 0)
+    indices = pyArborX.intView1D("indices", 0)
+
+    bvh.query(execution_space, queries, indices, offsets)
+
+    for i in range(offsets.size()-1):
+        print("[%d]" % i, end="")
+        for j in range(offsets[i], offsets[i+1]):
+            print(" %d" % indices[j], end="")
+        print("")
+
+    # As the Python garbage collector does not respect Kokkos finalize at this
+    # time, explicitly delete all ArborX structures
+    del bvh
+    del queries
+    del primitives
+    del indices
+    del offsets
+
+
+if __name__ == "__main__":
+    pyArborX.initialize()
+    pyArborX.printConfig()
+    run()
+    pyArborX.finalize()

static/CMakeLists.txt

@@ -1,39 +1,53 @@
 project(pyArborX_static LANGUAGES CXX)
 
-#choose modules that should be included in the build
+# Choose modules to be included
 set(pyArborX_STATIC_GEOMETRY_MODULES Point Box Sphere)
-set(pyArborX_STATIC_UTILITY_MODULES Experimental)
+set(pyArborX_STATIC_UTILITY_MODULES ExecutionSpace Experimental Util BVH)
+set(pyArborX_HACKY_VIEWS_MODULES IntersectView intView1D)
 
-# get source files for selected static modules
+# Get source files for selected static modules
+# NOTE: hacky views are in "config.hpp"
 foreach(PY_MODULE IN LISTS pyArborX_STATIC_GEOMETRY_MODULES pyArborX_STATIC_UTILITY_MODULES)
   list(APPEND pyArborX_SRC ${PROJECT_SOURCE_DIR}/src/pyArborX_${PY_MODULE}.cpp)
   list(APPEND MODULE_INCLUDES "\n#include \"pyArborX_${PY_MODULE}.hpp\"" )
   list(APPEND MODULE_GENERATORS "\npyArborX::generate${PY_MODULE}Wrapper(m)")
 endforeach()
 
-#generate bindings for views of ArborX types
-set(LAYOUTS LayoutLeft LayoutRight)
-set(MEMORYSPACES Default HostSpace)
+#
+# set(MEMORYSPACES Default HostSpace)
+set(MEMORYSPACES Default)
 file(MAKE_DIRECTORY ${PROJECT_BINARY_DIR}/generated_files)
-
 foreach(GEOMETRY IN LISTS pyArborX_STATIC_GEOMETRY_MODULES)
-  foreach(LAYOUT IN LISTS LAYOUTS)
-    foreach(MEMORYSPACE IN LISTS MEMORYSPACES)
-      set(VIEW_NAME "Kokkos_View_ArborX_${GEOMETRY}_1D_${LAYOUT}_${MEMORYSPACE}")
-      if (MEMORYSPACE STREQUAL Default)
-        set(VIEW_TYPE "Kokkos::View<ArborX::${GEOMETRY}*,Kokkos::${LAYOUT},Kokkos::${MEMORYSPACE}ExecutionSpace::memory_space>")
-      else()
-        set(VIEW_TYPE "Kokkos::View<ArborX::${GEOMETRY}*,Kokkos::${LAYOUT},Kokkos::${MEMORYSPACE}>")
-      endif()
-      set(VIEW_BASE_TYPE "ArborX::${GEOMETRY}")
-      set(VIEW_INCLUDE "\n#include \"pyArborX_${VIEW_NAME}.hpp\"")
-
-      configure_file(include/pyArborX_Views.hpp.in generated_files/pyArborX_${VIEW_NAME}.hpp)
-      configure_file(src/pyArborX_Views.cpp.in generated_files/pyArborX_${VIEW_NAME}.cpp)
-      list(APPEND pyArborX_SRC ${PROJECT_BINARY_DIR}/generated_files/pyArborX_${VIEW_NAME}.cpp)
-      list(APPEND MODULE_INCLUDES "\n#include \"pyArborX_${VIEW_NAME}.hpp\"" )
-      list(APPEND MODULE_GENERATORS "\npyArborX::generate${VIEW_NAME}Wrapper(m)")
-    endforeach()
+  foreach(MEMORYSPACE IN LISTS MEMORYSPACES)
+    set(VIEW_NAME "Kokkos_View_ArborX_${GEOMETRY}_1D_${MEMORYSPACE}")
+    if (MEMORYSPACE STREQUAL Default)
+      set(VIEW_TYPE "Kokkos::View<ArborX::${GEOMETRY}*,Kokkos::${MEMORYSPACE}ExecutionSpace::memory_space>")
+    else()
+      set(VIEW_TYPE "Kokkos::View<ArborX::${GEOMETRY}*,Kokkos::${MEMORYSPACE}>")
+    endif()
+    set(VIEW_BASE_TYPE "ArborX::${GEOMETRY}")
+    set(VIEW_INCLUDE "\n#include \"pyArborX_${VIEW_NAME}.hpp\"")
+
+    configure_file(include/pyArborX_Views.hpp.in generated_files/pyArborX_${VIEW_NAME}.hpp)
+    configure_file(src/pyArborX_Views.cpp.in generated_files/pyArborX_${VIEW_NAME}.cpp)
+    list(APPEND pyArborX_SRC ${PROJECT_BINARY_DIR}/generated_files/pyArborX_${VIEW_NAME}.cpp)
+    list(APPEND MODULE_INCLUDES "\n#include \"pyArborX_${VIEW_NAME}.hpp\"" )
+    list(APPEND MODULE_GENERATORS "\npyArborX::generate${VIEW_NAME}Wrapper(m)")
+  endforeach()
+endforeach()
+foreach(PY_VIEW IN LISTS pyArborX_HACKY_VIEWS_MODULES)
+  foreach(MEMORYSPACE IN LISTS MEMORYSPACES)
+    set(VIEW_NAME ${PY_VIEW})
+    set(VIEW_TYPE ${PY_VIEW}Type)
+    set(VIEW_BASE_TYPE ${PY_VIEW}BaseType)
+    set(VIEW_INCLUDE "\n#include \"pyArborX_${PY_VIEW}.hpp\"")
+
+    configure_file(include/pyArborX_Views.hpp.in generated_files/pyArborX_${PY_VIEW}.hpp)
+    configure_file(src/pyArborX_Views.cpp.in generated_files/pyArborX_${PY_VIEW}.cpp)
+
+    list(APPEND pyArborX_SRC ${PROJECT_BINARY_DIR}/generated_files/pyArborX_${VIEW_NAME}.cpp)
+    list(APPEND MODULE_INCLUDES "\n#include \"pyArborX_${VIEW_NAME}.hpp\"" )
+    list(APPEND MODULE_GENERATORS "\npyArborX::generate${VIEW_NAME}Wrapper(m)")
   endforeach()
 endforeach()
 
@@ -45,6 +59,6 @@ configure_file(pyArborX_static.cpp.in generated_files/pyArborX_static.cpp)
 PYBIND11_ADD_MODULE(pyArborX_static generated_files/pyArborX_static.cpp ${pyArborX_SRC})
 target_include_directories(pyArborX_static PUBLIC ${PROJECT_SOURCE_DIR}/include)
 target_include_directories(pyArborX_static PUBLIC ${PROJECT_BINARY_DIR}/generated_files)
-target_link_libraries(pyArborX_static PUBLIC ArborX::ArborX)
+target_link_libraries(pyArborX_static PUBLIC ArborX::ArborX INTERFACE Kokkos::kokkos)
 set_target_properties(pyArborX_static PROPERTIES
   LIBRARY_OUTPUT_DIRECTORY ${CMAKE_SOURCE_DIR}/pyArborX)

static/include/config.hpp

@@ -0,0 +1,36 @@
+#ifndef PYARBORX_CONFIG_H
+#define PYARBORX_CONFIG_H
+
+#include <ArborX_Point.hpp>
+#include <ArborX_Predicates.hpp>
+#include <ArborX_SpaceFillingCurves.hpp>
+#include <ArborX_Sphere.hpp>
+
+#include <Kokkos_Core.hpp>
+
+namespace pyArborX
+{
+
+// instantiation of all template arguments by hand, as there is no interface for
+// these ... for now
+using ExecutionSpace = Kokkos::DefaultExecutionSpace;
+using MemorySpace = ExecutionSpace::memory_space;
+// using MemorySpace = Kokkos::CudaUVMSpace;
+
+using intView1DBaseType = int;
+using intView1DType = Kokkos::View<int *, MemorySpace>;
+
+using PointViewBaseType = ArborX::Point;
+using PointViewType = Kokkos::View<PointViewBaseType *, MemorySpace>;
+
+using IntersectViewBaseType = decltype(ArborX::intersects(ArborX::Sphere{}));
+using IntersectViewType = Kokkos::View<IntersectViewBaseType *, MemorySpace>;
+
+using Primitives = PointViewType;
+using Predicates = IntersectViewType;
+
+using SpaceFillingCurve = ArborX::Experimental::Morton64;
+
+} // namespace pyArborX
+
+#endif

static/include/pyArborX_BVH.hpp

@@ -0,0 +1,16 @@
+#ifndef PYARBORX_BVH_HPP
+#define PYARBORX_BVH_HPP
+
+#include <ArborX_LinearBVH.hpp>
+
+#include "config.hpp"
+#include <pybind11/pybind11.h>
+
+namespace pyArborX
+{
+
+void generateBVHWrapper(pybind11::module &m);
+
+}
+
+#endif

static/include/pyArborX_Box.hpp

@@ -3,10 +3,9 @@
 
 #include <ArborX_Box.hpp>
 
-#include <pybind11/pybind11.h>
-#include <string.h>
+#include <string>
 
-namespace py = pybind11;
+#include <pybind11/pybind11.h>
 
 namespace pyArborX
 {
@@ -15,7 +14,8 @@ namespace helper
 std::string pyPrintBox(ArborX::Box const &b);
 }
 
-void generateBoxWrapper(py::module &m);
+void generateBoxWrapper(pybind11::module &m);
+
 } // namespace pyArborX
 
 #endif

static/include/pyArborX_ExecutionSpace.hpp

@@ -0,0 +1,13 @@
+#ifndef PYARBORX_EXECUTION_SPACE_HPP
+#define PYARBORX_EXECUTION_SPACE_HPP
+
+#include <pybind11/pybind11.h>
+
+namespace pyArborX
+{
+
+void generateExecutionSpaceWrapper(pybind11::module &m);
+
+}
+
+#endif

static/include/pyArborX_Experimental.hpp

@@ -5,12 +5,11 @@
 
 #include <pybind11/pybind11.h>
 
-namespace py = pybind11;
-
 namespace pyArborX
 {
 
-void generateExperimentalWrapper(py::module &m);
+void generateExperimentalWrapper(pybind11::module &m);
 
 } // namespace pyArborX
+
 #endif

static/include/pyArborX_Point.hpp

@@ -3,10 +3,9 @@
 
 #include <ArborX_Point.hpp>
 
-#include <pybind11/pybind11.h>
-#include <string.h>
+#include <string>
 
-namespace py = pybind11;
+#include <pybind11/pybind11.h>
 
 namespace pyArborX
 {
@@ -15,7 +14,7 @@ namespace helper
 std::string pyPrintPoint(ArborX::Point const &p);
 }
 
-void generatePointWrapper(py::module &m);
+void generatePointWrapper(pybind11::module &m);
 } // namespace pyArborX
 
 #endif

static/include/pyArborX_Sphere.hpp

@@ -3,10 +3,9 @@
 
 #include <ArborX_Sphere.hpp>
 
-#include <pybind11/pybind11.h>
-#include <string.h>
+#include <string>
 
-namespace py = pybind11;
+#include <pybind11/pybind11.h>
 
 namespace pyArborX
 {
@@ -15,7 +14,7 @@ namespace helper
 std::string pyPrintSphere(ArborX::Sphere const &s);
 }
 
-void generateSphereWrapper(py::module &m);
+void generateSphereWrapper(pybind11::module &m);
 } // namespace pyArborX
 
 #endif

static/include/pyArborX_Util.hpp

@@ -0,0 +1,21 @@
+#ifndef PYARBORX_UTIL_HPP
+#define PYARBORX_UTIL_HPP
+
+#include "config.hpp"
+#include <pybind11/pybind11.h>
+
+namespace pyArborX
+{
+
+namespace helper
+{
+Predicates generateWithinQueries_device(ExecutionSpace execution_space,
+                                        Primitives query_pts_view,
+                                        int n_queries, float radius);
+}
+
+void generateUtilWrapper(pybind11::module &m);
+
+} // namespace pyArborX
+
+#endif

static/include/pyArborX_Views.hpp.in

@@ -3,12 +3,10 @@
 
 #include <pybind11/pybind11.h>
 
-namespace py = pybind11;
-
 namespace pyArborX
 {
 
-void generate@VIEW_NAME@Wrapper(py::module & m);
+void generate@VIEW_NAME@Wrapper(pybind11::module &m);
 
 }
 #endif

static/include/pyArborX_Views_Util.hpp

@@ -0,0 +1,23 @@
+#ifndef PYARBORX_VIEW_UTIL_HPP
+#define PYARBORX_VIEW_UTIL_HPP
+
+#include <Kokkos_Core.hpp>
+
+namespace pyArborX
+{
+
+template <typename ViewType>
+auto create_mirror_view(ViewType const &source)
+{
+  return Kokkos::create_mirror_view(source);
+}
+
+template <typename ViewDest, typename ViewSrc>
+auto deep_copy(ViewDest const &dest, ViewSrc const &src)
+{
+  return Kokkos::deep_copy(dest, src);
+}
+
+} // namespace pyArborX
+
+#endif

static/pyArborX_static.cpp.in

@@ -1,15 +1,16 @@
+#include <Kokkos_Core.hpp>
+
 #include <pybind11/pybind11.h>
 
 @MODULE_INCLUDES@
 
-
-namespace py = pybind11;
-
-PYBIND11_MODULE(pyArborX_static, m) {
+PYBIND11_MODULE(pyArborX_static, m)
+{
   m.attr("__name__") = "pyArborX_static";
 
+  m.def("initialize", []() { Kokkos::initialize(); });
   m.def("printConfig", []() { Kokkos::print_configuration(std::cout); });
+  m.def("finalize", &Kokkos::finalize);
 
   @MODULE_GENERATORS@;
-
 }