Bp implementation

.github/workflows/build-test.yml

@@ -32,6 +32,10 @@ jobs:
       working-directory: ./build
       run: ./louds_tree_tests
 
+    - name: Run BP Tree Tests
+      working-directory: ./build
+      run: ./bp_tree_tests
+
     - name: Run DFUDS Tree Tests
       working-directory: ./build
       run: ./dfuds_tree_tests
@@ -96,6 +100,18 @@ jobs:
         fi
         exit $rc
 
+    - name: Run BP Tree Tests
+      working-directory: ./build
+      run: |
+        timeout 1800 sde-external-9.58.0-2025-06-16-lin/sde64 -icl -emu-xinuse 0 -- \
+          ./bp_tree_tests --gtest_output=xml:bp_results.xml
+        rc=$?
+        if [ $rc -eq 124 ] && grep -q 'failures="0"' bp_results.xml 2>/dev/null; then
+          echo "SDE timed out during process teardown (known SDE/ASan issue) - all tests passed, treating as success"
+          exit 0
+        fi
+        exit $rc
+
     - name: Run DFUDS Tree Tests
       working-directory: ./build
       run: |

CMakeLists.txt

@@ -175,6 +175,15 @@ if(PIXIE_TESTS)
         gtest_main
         ${PIXIE_DIAGNOSTICS_LIBS})
 
+    add_executable(bp_tree_tests
+            src/tests/bp_tree_tests.cpp)
+    target_include_directories(bp_tree_tests
+            PUBLIC include)
+    target_link_libraries(bp_tree_tests
+            gtest
+            gtest_main
+            ${PIXIE_DIAGNOSTICS_LIBS})
+
     add_executable(dfuds_tree_tests
             src/tests/dfuds_tree_tests.cpp)
     target_include_directories(dfuds_tree_tests
@@ -239,6 +248,15 @@ if(PIXIE_BENCHMARKS)
         benchmark_main
         ${PIXIE_DIAGNOSTICS_LIBS})
 
+    add_executable(bp_tree_benchmarks
+            src/benchmarks/bp_tree_benchmarks.cpp)
+    target_include_directories(bp_tree_benchmarks
+            PUBLIC include)
+    target_link_libraries(bp_tree_benchmarks
+            benchmark
+            benchmark_main
+            ${PIXIE_DIAGNOSTICS_LIBS})
+
     add_executable(dfuds_tree_benchmarks
             src/benchmarks/dfuds_tree_benchmarks.cpp)
     target_include_directories(dfuds_tree_benchmarks

CMakePresets.json

@@ -114,6 +114,7 @@
                 "benchmark_tests",
                 "test_rmm",
                 "louds_tree_tests",
+                "bp_tree_tests",
                 "dfuds_tree_tests",
                 "excess_positions_tests"
             ]
@@ -127,6 +128,7 @@
                 "benchmark_tests",
                 "test_rmm",
                 "louds_tree_tests",
+                "bp_tree_tests",
                 "dfuds_tree_tests",
                 "excess_positions_tests"
             ]
@@ -139,6 +141,7 @@
                 "benchmarks",
                 "bench_rmm",
                 "louds_tree_benchmarks",
+                "bp_tree_benchmarks",
                 "dfuds_tree_benchmarks",
                 "alignment_comparison",
                 "excess_positions_benchmarks"
@@ -153,6 +156,7 @@
                 "bench_rmm",
                 "bench_rmm_sdsl",
                 "louds_tree_benchmarks",
+                "bp_tree_benchmarks",
                 "dfuds_tree_benchmarks",
                 "alignment_comparison",
                 "excess_positions_benchmarks"
@@ -166,6 +170,7 @@
                 "benchmarks",
                 "bench_rmm",
                 "louds_tree_benchmarks",
+                "bp_tree_benchmarks",
                 "dfuds_tree_benchmarks",
                 "alignment_comparison",
                 "excess_positions_benchmarks"
@@ -188,6 +193,7 @@
                 "benchmark_tests",
                 "test_rmm",
                 "louds_tree_tests",
+                "bp_tree_tests",
                 "dfuds_tree_tests",
                 "excess_positions_tests"
             ]
@@ -201,6 +207,7 @@
                 "benchmark_tests",
                 "test_rmm",
                 "louds_tree_tests",
+                "bp_tree_tests",
                 "dfuds_tree_tests",
                 "excess_positions_tests"
             ]

include/pixie/bp_tree.h

@@ -0,0 +1,171 @@
+#pragma once
+
+#include <pixie/rmm_tree.h>
+
+#include <cstdint>
+
+#include "utils.h"
+
+namespace pixie {
+
+/**
+ * @brief A tree class based on the balances parentheses (BP)
+ * representation
+ */
+class BPTree {
+ private:
+  const size_t num_bits_;
+  RmMTree rmm;
+
+ public:
+  /**
+   * @brief A node class of BP tree
+   */
+  struct Node {
+    size_t number;
+    size_t pos;
+
+    /**
+     * @brief A node class of BP tree
+     */
+    Node(size_t node_number, size_t bp_pos)
+        : number(node_number), pos(bp_pos) {}
+  };
+
+  /**
+   * @brief Constructor from an external array of uint64_t
+   */
+  explicit BPTree(const std::vector<std::uint64_t>& words, size_t tree_size)
+      : num_bits_(2 * tree_size), rmm(words, 2 * tree_size) {}
+
+  /**
+   * @brief Returns the root node
+   */
+  Node root() const { return Node(0, 0); }
+
+  /**
+   * @brief Returns the size of the tree
+   */
+  size_t size() const { return num_bits_ / 2; }
+
+  /**
+   * @brief Indicates if @p node is a leaf
+   */
+  bool is_leaf(const Node& node) const {
+    return (node.pos + 2 == num_bits_) or rmm.bit(node.pos + 1) == 0;
+  }
+
+  /**
+   * @brief Indicates if @p node is a root
+   */
+  bool is_root(const Node& node) { return node.number == 0; }
+
+  /**
+   * @brief Returns the number of children of a @p node
+   *    this method has O(d) time complexity!
+   *
+   *    TODO try make this faster
+   */
+  size_t degree(const Node& node) const {
+    if (is_leaf(node)) {
+      return 0;
+    }
+    Node child = first_child(node);
+    size_t child_count = 1;
+    while (true) {
+      if (is_last_child(child)) {
+        return child_count;
+      }
+      child = next_sibling(child);
+      child_count++;
+    }
+  }
+
+  /**
+   * @brief Returns first child of a @p node
+   */
+  Node first_child(const Node& node) const {
+    size_t pos = node.pos + 1;
+    size_t num = node.number + 1;
+    return Node(num, pos);
+  }
+
+  /**
+   * @brief Returns the i-th child of @p node
+   * Indexing starts at 0
+   *    this method has O(i) time complexity!
+   *
+   *    TODO try make this faster
+   */
+  Node child(const Node& node, size_t i) const {
+    Node child = first_child(node);
+    while (i--) {
+      child = next_sibling(child);
+    }
+    return child;
+  }
+
+  /**
+   * @brief Returns the parent of a @p node if @p node is not root,
+   * else returns root
+   */
+  Node parent(const Node& node) const {
+    if (node.number == 0) {
+      return root();
+    }
+    size_t pos = rmm.enclose(node.pos);
+    size_t num = rmm.rank1(pos);
+    return Node(num, pos);
+  }
+
+  /**
+   * @brief Indicates if @p node is last child
+   */
+  bool is_last_child(const Node& node) const {
+    size_t end = rmm.close(node.pos);
+
+    return end + 2 >= num_bits_ or rmm.bit(end + 1) == 0;
+  }
+
+  /**
+   * @brief Returns next sibling of a @p node
+   */
+  Node next_sibling(const Node& node) const {
+    size_t pos = rmm.close(node.pos) + 1;
+    size_t num = rmm.rank1(pos + 1) - 1;
+    return Node(num, pos);
+  }
+};
+
+std::vector<uint64_t> adj_to_bp(size_t tree_size,
+                                const std::vector<std::vector<size_t>>& adj) {
+  size_t bp_size = tree_size * 2;
+  std::vector<uint64_t> bp((bp_size + 63) / 64, 0);
+  std::vector<std::pair<size_t, size_t>> stack;
+  stack.push_back(std::make_pair(0, 0));
+  size_t pos = 0;
+  bp[pos >> 6] = bp[pos >> 6] | (1ULL << (pos & 63));
+  while (!stack.empty()) {
+    auto& [v, p] = stack.back();
+    p++;
+    if (p >= adj[v].size()) {
+      pos++;
+      stack.pop_back();
+      continue;
+    }
+    pos++;
+    bp[pos >> 6] = bp[pos >> 6] | (1ULL << (pos & 63));
+    stack.push_back(std::make_pair(adj[v][p], 0));
+  }
+  return bp;
+}
+
+bool operator==(const AdjListNode& a, const BPTree::Node& b) {
+  return a.number == b.number;
+}
+
+bool operator==(const BPTree::Node& b, const AdjListNode& a) {
+  return a.number == b.number;
+}
+
+}  // namespace pixie

include/pixie/utils.h

@@ -30,7 +30,7 @@ std::vector<std::vector<size_t>> bfs_order(
   std::queue<std::pair<size_t, size_t>> q;
   bfs_adj[0].push_back(0);
   q.push({0, 0});
-  int cnt = 1;
+  size_t cnt = 1;
   while (!q.empty()) {
     size_t old_v = q.front().first;
     size_t cur_v = q.front().second;

scripts/coverage_report.sh

@@ -10,6 +10,7 @@ cmake --build --preset coverage
 "${BUILD_DIR}/unittests"
 "${BUILD_DIR}/excess_positions_tests"
 "${BUILD_DIR}/louds_tree_tests"
+"${BUILD_DIR}/bp_tree_tests"
 "${BUILD_DIR}/dfuds_tree_tests"
 "${BUILD_DIR}/test_rmm"
 

src/benchmarks/bp_tree_benchmarks.cpp

@@ -0,0 +1,66 @@
+#include <benchmark/benchmark.h>
+#include <pixie/bp_tree.h>
+#include <pixie/utils.h>
+
+#include <random>
+
+using Node = pixie::BpTree::Node;
+using pixie::BpTree;
+
+/**
+ * DFS with O(1) extra memory
+ */
+static void BM_BpTreeDFS(benchmark::State& state) {
+  size_t tree_size = state.range(0);
+  std::mt19937_64 rng(42);
+
+  for (auto _ : state) {
+    state.PauseTiming();
+    std::vector<std::vector<size_t>> adj = generate_random_tree(tree_size, rng);
+    adj = dfs_order(tree_size, adj);
+    std::vector<uint64_t> bp = adj_to_bp(tree_size, adj);
+    BpTree tree(bp, tree_size);
+
+    Node cur = tree.root();
+    bool above = 1;
+
+    state.ResumeTiming();
+
+    benchmark::DoNotOptimize(cur);
+
+    while (true) {
+      if (above) {
+        if (tree.is_leaf(cur)) {
+          above = 0;
+        } else {
+          cur = tree.first_child(cur);
+        }
+        benchmark::DoNotOptimize(cur);
+      } else {
+        if (tree.is_last_child(cur)) {
+          cur = tree.parent(cur);
+          if (tree.is_root(cur)) {
+            break;
+          }
+          benchmark::DoNotOptimize(cur);
+        } else {
+          cur = tree.next_sibling(cur);
+          above = 1;
+          benchmark::DoNotOptimize(cur);
+        }
+      }
+    }
+  }
+}
+
+BENCHMARK(BM_BpTreeDFS)
+    ->ArgNames({"tree_size"})
+    ->RangeMultiplier(2)
+    ->Range(1ull << 8, 1ull << 18)
+    ->Iterations(100);
+
+BENCHMARK(BM_BpTreeDFS)
+    ->ArgNames({"tree_size"})
+    ->RangeMultiplier(2)
+    ->Range(1ull << 18, 1ull << 26)
+    ->Iterations(10);