Merge Segmented Array

This merge adds a class to store a segmented array. A flat ginkgo array is partitioned into multiple segments by an additional index offset array. The segment `i` starts within the flat buffer at index `offsets[i]`, and ends (exclusively) at index `offsets[i + 1]`. The class only provides access to the flat buffer and the offsets.

Related PR: #1545

core/CMakeLists.txt

@@ -16,6 +16,7 @@ target_sources(ginkgo
     base/mpi.cpp
     base/mtx_io.cpp
     base/perturbation.cpp
+    base/segmented_array.cpp
     base/timer.cpp
     base/version.cpp
     config/property_tree.cpp

core/base/segmented_array.cpp

@@ -0,0 +1,187 @@
+// SPDX-FileCopyrightText: 2017 - 2024 The Ginkgo authors
+//
+// SPDX-License-Identifier: BSD-3-Clause
+
+#include <ginkgo/core/base/segmented_array.hpp>
+
+
+#include "core/base/array_access.hpp"
+#include "core/components/prefix_sum_kernels.hpp"
+
+
+namespace gko {
+namespace {
+
+
+GKO_REGISTER_OPERATION(prefix_sum, components::prefix_sum_nonnegative);
+
+
+}
+
+
+template <typename T>
+size_type segmented_array<T>::get_size() const
+{
+    return buffer_.get_size();
+}
+
+
+template <typename T>
+size_type segmented_array<T>::get_segment_count() const
+{
+    return offsets_.get_size() ? offsets_.get_size() - 1 : 0;
+}
+
+
+template <typename T>
+T* segmented_array<T>::get_flat_data()
+{
+    return buffer_.get_data();
+}
+
+
+template <typename T>
+const T* segmented_array<T>::get_const_flat_data() const
+{
+    return buffer_.get_const_data();
+}
+
+
+template <typename T>
+const gko::array<int64>& segmented_array<T>::get_offsets() const
+{
+    return offsets_;
+}
+
+
+template <typename T>
+std::shared_ptr<const Executor> segmented_array<T>::get_executor() const
+{
+    return buffer_.get_executor();
+}
+
+
+template <typename T>
+segmented_array<T>::segmented_array(std::shared_ptr<const Executor> exec)
+    : buffer_(exec), offsets_(exec, 1)
+{
+    offsets_.fill(0);
+}
+
+
+array<int64> sizes_to_offsets(const gko::array<int64>& sizes)
+{
+    auto exec = sizes.get_executor();
+    array<int64> offsets(exec, sizes.get_size() + 1);
+    exec->copy(sizes.get_size(), sizes.get_const_data(), offsets.get_data());
+    exec->run(make_prefix_sum(offsets.get_data(), offsets.get_size()));
+    return offsets;
+}
+
+
+template <typename T>
+segmented_array<T> segmented_array<T>::create_from_sizes(
+    const gko::array<int64>& sizes)
+{
+    return create_from_offsets(sizes_to_offsets(sizes));
+}
+
+
+template <typename T>
+segmented_array<T> segmented_array<T>::create_from_sizes(
+    gko::array<T> buffer, const gko::array<int64>& sizes)
+{
+    return create_from_offsets(std::move(buffer), sizes_to_offsets(sizes));
+}
+
+
+template <typename T>
+segmented_array<T> segmented_array<T>::create_from_offsets(
+    gko::array<int64> offsets)
+{
+    GKO_THROW_IF_INVALID(offsets.get_size() > 0,
+                         "The offsets for segmented_arrays require at least "
+                         "one element.");
+    auto size =
+        static_cast<size_type>(get_element(offsets, offsets.get_size() - 1));
+    return create_from_offsets(array<T>{offsets.get_executor(), size},
+                               std::move(offsets));
+}
+
+
+template <typename T>
+segmented_array<T> segmented_array<T>::create_from_offsets(
+    gko::array<T> buffer, gko::array<int64> offsets)
+{
+    GKO_ASSERT_EQ(buffer.get_size(),
+                  get_element(offsets, offsets.get_size() - 1));
+    segmented_array<T> result(buffer.get_executor());
+    result.offsets_ = std::move(offsets);
+    result.buffer_ = std::move(buffer);
+    return result;
+}
+
+
+template <typename T>
+segmented_array<T>::segmented_array(std::shared_ptr<const Executor> exec,
+                                    segmented_array&& other)
+    : segmented_array(exec)
+{
+    *this = std::move(other);
+}
+
+
+template <typename T>
+segmented_array<T>::segmented_array(std::shared_ptr<const Executor> exec,
+                                    const segmented_array& other)
+    : segmented_array(exec)
+{
+    *this = other;
+}
+
+
+template <typename T>
+segmented_array<T>::segmented_array(const segmented_array& other)
+    : segmented_array(other.get_executor())
+{
+    *this = other;
+}
+
+
+template <typename T>
+segmented_array<T>::segmented_array(segmented_array&& other)
+    : segmented_array(other.get_executor())
+{
+    *this = std::move(other);
+}
+
+
+template <typename T>
+segmented_array<T>& segmented_array<T>::operator=(const segmented_array& other)
+{
+    if (this != &other) {
+        buffer_ = other.buffer_;
+        offsets_ = other.offsets_;
+    }
+    return *this;
+}
+
+
+template <typename T>
+segmented_array<T>& segmented_array<T>::operator=(segmented_array&& other)
+{
+    if (this != &other) {
+        buffer_ = std::move(other.buffer_);
+        offsets_ = std::exchange(other.offsets_,
+                                 array<int64>{other.get_executor(), {0}});
+    }
+    return *this;
+}
+
+
+#define GKO_DECLARE_SEGMENTED_ARRAY(_type) class segmented_array<_type>
+
+GKO_INSTANTIATE_FOR_EACH_POD_TYPE(GKO_DECLARE_SEGMENTED_ARRAY);
+
+
+}  // namespace gko

core/base/segmented_array.hpp

@@ -0,0 +1,57 @@
+// SPDX-FileCopyrightText: 2017 - 2024 The Ginkgo authors
+//
+// SPDX-License-Identifier: BSD-3-Clause
+
+#ifndef GINKGO_SEGMENTED_ARRAY_HPP
+#define GINKGO_SEGMENTED_ARRAY_HPP
+
+
+#include <ginkgo/core/base/segmented_array.hpp>
+
+
+namespace gko {
+
+
+/**
+ * Helper struct storing an array segment
+ *
+ * @tparam T  The value type of the array
+ */
+template <typename T>
+struct array_segment {
+    T* begin;
+    T* end;
+};
+
+
+/**
+ * Helper function to create a device-compatible view of an array segment.
+ */
+template <typename T>
+constexpr array_segment<T> get_array_segment(segmented_array<T>& sarr,
+                                             size_type segment_id)
+{
+    assert(segment_id < sarr.get_segment_count());
+    auto offsets = sarr.get_offsets().get_const_data();
+    auto data = sarr.get_flat_data();
+    return {data + offsets[segment_id], data + offsets[segment_id + 1]};
+}
+
+
+/**
+ * Helper function to create a device-compatible view of a const array segment.
+ */
+template <typename T>
+constexpr array_segment<const T> get_array_segment(
+    const segmented_array<T>& sarr, size_type segment_id)
+{
+    assert(segment_id < sarr.get_segment_count());
+    auto offsets = sarr.get_offsets().get_const_data();
+    auto data = sarr.get_const_flat_data();
+    return {data + offsets[segment_id], data + offsets[segment_id + 1]};
+}
+
+
+}  // namespace gko
+
+#endif  // GINKGO_SEGMENTED_ARRAY_HPP

core/test/base/CMakeLists.txt

@@ -26,6 +26,7 @@ ginkgo_create_test(polymorphic_object)
 ginkgo_create_test(range)
 ginkgo_create_test(range_accessors)
 ginkgo_create_test(sanitizers ADDITIONAL_LIBRARIES Threads::Threads)
+ginkgo_create_test(segmented_array)
 ginkgo_create_test(types)
 ginkgo_create_test(utils)
 ginkgo_create_test(version EXECUTABLE_NAME version_test) # version collides with C++ stdlib header