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mperikovmperikov
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Louds implementation (#26)
1 parent 221b5f0 commit 46ee754

17 files changed

Lines changed: 905 additions & 1 deletion

‎.github/workflows/build-test.yml‎

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@@ -27,6 +27,10 @@ jobs:
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- name: Run Unittests
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working-directory: ./build
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run: ./unittests
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- name: Run LOUDS Tree Tests
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working-directory: ./build
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run: ./louds_tree_tests
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build-and-test-with-SDE:
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runs-on: ubuntu-latest
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- name: Run Unittests
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working-directory: ./build
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run: sde-external-9.58.0-2025-06-16-lin/sde64 -icl -emu-xinuse 0 -- ./unittests
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run: sde-external-9.58.0-2025-06-16-lin/sde64 -icl -emu-xinuse 0 -- ./unittests
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- name: Run LOUDS Tree Tests
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working-directory: ./build
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run: sde-external-9.58.0-2025-06-16-lin/sde64 -icl -emu-xinuse 0 -- ./louds_tree_tests

‎CMakeLists.txt‎

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@@ -94,6 +94,20 @@ target_include_directories(bench_rmm
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target_link_libraries(bench_rmm
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benchmark)
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add_executable(louds_tree_benchmarks
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src/louds_tree_benchmarks.cpp)
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target_include_directories(louds_tree_benchmarks
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PUBLIC include
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)
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target_link_libraries(louds_tree_benchmarks
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benchmark
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benchmark_main
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)
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add_executable(test_rmm
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src/test_rmm.cpp)
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target_include_directories(test_rmm
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gtest
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gtest_main)
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add_executable(louds_tree_tests
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src/louds_tree_tests.cpp)
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target_include_directories(louds_tree_tests
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PUBLIC include
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PUBLIC ${GOOGLETEST_SOURCE_DIR}/include
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)
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target_link_libraries(louds_tree_tests
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gtest
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gtest_main)
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add_executable(alignment_comparison
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src/alignment_comparison.cpp)

‎include/louds_tree.h‎

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#pragma once
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#include <cstdint>
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#include <span>
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#include "bitvector.h"
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namespace pixie {
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/**
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* @brief A node class of LOUDS tree
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*/
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struct LoudsNode {
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size_t number;
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size_t pos;
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LoudsNode(size_t node_number, size_t louds_pos)
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: number(node_number), pos(louds_pos) {}
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};
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/**
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* @brief A tree class based on the level order unary degree sequence (LOUDS)
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* representation
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*/
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class LoudsTree {
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private:
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BitVector bv;
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public:
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/**
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* @brief Constructor from an external array of uint64_t
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*/
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explicit LoudsTree(std::span<const uint64_t> louds, size_t tree_size)
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: bv(louds, 2 * tree_size - 1) {}
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/**
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* @brief Returns the root node
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*/
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LoudsNode root() const { return LoudsNode(0, 0); }
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/**
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* @brief Returns the size of the tree
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*/
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size_t size() const { return (bv.size() + 1) / 2; }
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/**
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* @brief Indicates if @p node is a leaf
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*/
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bool is_leaf(const LoudsNode& node) const {
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return (node.pos + 1 == bv.size()) or bv[node.pos + 1];
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}
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/**
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* @brief Indicates if @p node is a root
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*/
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bool is_root(const LoudsNode& node) const { return node.number == 0; }
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/**
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* @brief Returns the number of children of a @p node
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*/
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size_t degree(const LoudsNode& node) const {
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if (is_leaf(node)) {
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return 0;
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}
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return bv.select(node.number + 2) - node.pos - 1;
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}
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/**
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* @brief Returns the i-th child of @p node
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* Indexing starts at 0
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*/
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LoudsNode child(const LoudsNode& node, size_t i) const {
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size_t zeros = node.pos + i + 1 - node.number;
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return LoudsNode(zeros, bv.select(zeros + 1));
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}
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/**
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* @brief Returns first child of a @p node
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*/
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LoudsNode first_child(const LoudsNode& node) const {
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size_t zeros = node.pos + 1 - node.number;
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return LoudsNode(zeros, bv.select(zeros + 1));
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}
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/**
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* @brief Returns the parent of a @p node if @p node is not root,
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* else returns root
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*/
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LoudsNode parent(const LoudsNode& node) const {
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if (node.number == 0) {
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return root();
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}
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size_t zero_pos = bv.select0(node.number);
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size_t parent_number = zero_pos - node.number;
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return LoudsNode(parent_number, bv.select(parent_number + 1));
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}
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/**
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* @brief Indicates if @p node is last child
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*/
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bool is_last_child(const LoudsNode& node) const {
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size_t zero_pos = bv.select0(node.number);
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return bv[zero_pos + 1];
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}
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/**
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* @brief Returns next sibling of a @p node
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*/
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LoudsNode next_sibling(const LoudsNode& node) const {
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size_t sibling_number = node.number + 1;
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return LoudsNode(sibling_number, bv.select(sibling_number + 1));
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}
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};
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} // namespace pixie

‎include/utils.h‎

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#pragma once
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#include <queue>
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#include <random>
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#include <vector>
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#include "louds_tree.h"
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using pixie::LoudsNode;
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std::vector<std::vector<size_t>> generate_random_tree(size_t tree_size,
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std::mt19937_64& rng) {
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if (tree_size == 0) {
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return {};
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}
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std::vector<std::vector<size_t>> adj(tree_size);
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adj[0].push_back(0);
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for (size_t i = 1; i < tree_size; i++) {
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size_t parent = rng() % i;
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adj[i].push_back(parent);
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adj[parent].push_back(i);
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}
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return adj;
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}
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std::vector<std::vector<size_t>> bfs_order(
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size_t tree_size,
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const std::vector<std::vector<size_t>>& adj) {
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std::vector<std::vector<size_t>> bfs_adj(tree_size);
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std::queue<std::pair<size_t, size_t>> q;
31+
bfs_adj[0].push_back(0);
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q.push({0, 0});
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int cnt = 1;
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while (!q.empty()) {
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size_t old_v = q.front().first;
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size_t cur_v = q.front().second;
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q.pop();
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for (size_t i = 1; i < adj[old_v].size(); i++) {
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size_t old_u = adj[old_v][i];
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size_t cur_u = cnt++;
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q.push({old_u, cur_u});
42+
bfs_adj[cur_u].push_back(cur_v);
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bfs_adj[cur_v].push_back(cur_u);
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}
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}
46+
return bfs_adj;
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}
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std::vector<uint64_t> adj_to_louds(
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size_t tree_size,
51+
const std::vector<std::vector<size_t>>& adj) {
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size_t louds_size = tree_size * 2 - 1;
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std::vector<uint64_t> louds((louds_size + 63) / 64, 0);
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size_t pos = 0;
55+
for (size_t i = 0; i < tree_size; i++) {
56+
louds[pos >> 6] = louds[pos >> 6] | (1ULL << (pos & 63));
57+
pos += adj[i].size();
58+
}
59+
return louds;
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}
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struct AdjListNode {
63+
size_t number;
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};
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bool operator==(const AdjListNode& a, const LoudsNode& b) {
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return a.number == b.number;
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}
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bool operator==(const LoudsNode& b, const AdjListNode& a) {
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return a.number == b.number;
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}
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class AdjListTree {
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private:
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std::vector<std::vector<size_t>> adj;
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public:
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/**
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* @brief Constructor from adjacency list (root is 0)
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*/
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explicit AdjListTree(const std::vector<std::vector<size_t>>& adjacency_list)
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: adj(adjacency_list) {}
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/**
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* @brief Returns the root node
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*/
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AdjListNode root() const { return AdjListNode(0); }
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/**
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* @brief Checks if @p node is a leaf
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*/
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bool is_leaf(const AdjListNode& node) const {
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return adj[node.number].size() <= 1;
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}
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/**
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* @brief Checks if @p node is a root
99+
*/
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bool is_root(const AdjListNode& node) const { return node.number == 0; }
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/**
103+
* @brief Returns the number of children of @p node
104+
*/
105+
size_t degree(const AdjListNode& node) const {
106+
return adj[node.number].size() - 1;
107+
}
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/**
110+
* @brief Returns the i-th child of @p node
111+
* Indexing starts at 0
112+
*/
113+
AdjListNode child(const AdjListNode& node, size_t i) const {
114+
return AdjListNode(adj[node.number][i + 1]);
115+
}
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/**
118+
* @brief Returns the first child of @p node
119+
*/
120+
AdjListNode first_child(const AdjListNode& node) const {
121+
return AdjListNode(adj[node.number][1]);
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}
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/**
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* @brief Returns the parent of a @p node if @p node is not root,
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* else returns root
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*/
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AdjListNode parent(const AdjListNode& node) const {
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return AdjListNode(adj[node.number][0]);
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}
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/**
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* @brief Indicates if @p node is last child
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*/
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bool is_last_child(const AdjListNode& node) const {
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size_t p = parent(node).number;
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return adj[p].back() == node.number;
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}
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/**
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* @brief Returns next sibling of a @p node
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*/
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AdjListNode next_sibling(const AdjListNode& node) const {
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return AdjListNode(node.number + 1);
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}
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};

‎report/data/dfs.txt‎

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BM_LoudsTreeDFS/tree_size:256/iterations:10 17158 ns 15960 ns 10
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BM_LoudsTreeDFS/tree_size:512/iterations:10 32205 ns 30170 ns 10
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BM_LoudsTreeDFS/tree_size:1024/iterations:10 64570 ns 60450 ns 10
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BM_LoudsTreeDFS/tree_size:2048/iterations:10 149284 ns 139960 ns 10
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BM_LoudsTreeDFS/tree_size:4096/iterations:10 306694 ns 287710 ns 10
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BM_LoudsTreeDFS/tree_size:8192/iterations:10 639481 ns 599620 ns 10
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BM_LoudsTreeDFS/tree_size:16384/iterations:10 1321981 ns 1239680 ns 10
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BM_LoudsTreeDFS/tree_size:32768/iterations:10 2621919 ns 2458610 ns 10
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BM_LoudsTreeDFS/tree_size:65536/iterations:10 5418396 ns 5081010 ns 10
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BM_LoudsTreeDFS/tree_size:131072/iterations:10 11477777 ns 10762480 ns 10
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BM_LoudsTreeDFS/tree_size:262144/iterations:10 22475017 ns 21071420 ns 10
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BM_LoudsTreeDFS/tree_size:524288/iterations:10 51507287 ns 48337760 ns 10
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BM_LoudsTreeDFS/tree_size:1048576/iterations:10 139215927 ns 130654490 ns 10
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BM_LoudsTreeDFS/tree_size:2097152/iterations:10 274188404 ns 257485140 ns 10
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BM_LoudsTreeDFS/tree_size:4194304/iterations:10 393504994 ns 379028300 ns 10
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BM_LoudsTreeDFS/tree_size:8388608/iterations:10 772261790 ns 742915900 ns 10
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BM_LoudsTreeDFS/tree_size:16777216/iterations:10 1924302888 ns 1847300630 ns 10
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BM_LoudsTreeDFS/tree_size:33554432/iterations:10 4033885540 ns 3862881520 ns 10
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BM_AdjListTreeDFS/tree_size:256/iterations:10 7004 ns 6500 ns 10
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BM_AdjListTreeDFS/tree_size:512/iterations:10 12709 ns 11890 ns 10
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BM_AdjListTreeDFS/tree_size:1024/iterations:10 27121 ns 25400 ns 10
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BM_AdjListTreeDFS/tree_size:2048/iterations:10 61831 ns 57990 ns 10
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BM_AdjListTreeDFS/tree_size:4096/iterations:10 173807 ns 163320 ns 10
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BM_AdjListTreeDFS/tree_size:8192/iterations:10 346847 ns 325820 ns 10
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BM_AdjListTreeDFS/tree_size:16384/iterations:10 697983 ns 655640 ns 10
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BM_AdjListTreeDFS/tree_size:32768/iterations:10 1422141 ns 1336020 ns 10
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BM_AdjListTreeDFS/tree_size:65536/iterations:10 2862014 ns 2688070 ns 10
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BM_AdjListTreeDFS/tree_size:131072/iterations:10 6096719 ns 5727260 ns 10
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BM_AdjListTreeDFS/tree_size:262144/iterations:10 13984236 ns 13137420 ns 10
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BM_AdjListTreeDFS/tree_size:524288/iterations:10 36108305 ns 33921960 ns 10
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BM_AdjListTreeDFS/tree_size:1048576/iterations:10 97158888 ns 91052080 ns 10
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BM_AdjListTreeDFS/tree_size:2097152/iterations:10 130849640 ns 122713210 ns 10
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BM_AdjListTreeDFS/tree_size:4194304/iterations:10 519976249 ns 492515650 ns 10
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BM_AdjListTreeDFS/tree_size:8388608/iterations:10 1076193064 ns 1019121630 ns 10
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BM_AdjListTreeDFS/tree_size:16777216/iterations:10 2151390243 ns 2036195610 ns 10
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BM_AdjListTreeDFS/tree_size:33554432/iterations:10 4386640878 ns 4148986820 ns 10

‎report/data/dfs_comparison.png‎

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‎report/data/load_comparison_256.png‎

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‎report/data/load_comparison_512.png‎

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