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Code Cleanup
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@Alex-W4
Alex-W4 committed Oct 23, 2024
1 parent 26b65af commit 036a590
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Showing 3 changed files with 519 additions and 516 deletions.
165 changes: 109 additions & 56 deletions fuzz/rtree_verification.cc
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,6 @@
#include <cista/mmap.h>
#include <cinttypes>
#include <cstring>
#include <filesystem>
#include <iostream>

#include "cista/containers/rtree.h"
Expand All @@ -11,20 +10,22 @@ extern "C" {
#include "dependencies/rtree_c/rtree_c.h"
}



using cista_rtree = cista::rtree<uint32_t, 2, double>;
using mm_rtree = cista::rtree<uint32_t, 2, double, 64, uint32_t, cista::mmap_vec_map>;

using mm_rtree =
cista::rtree<uint32_t, 2, double, 64, uint32_t, cista::mmap_vec_map>;

// Struct for tracking found entities
struct ctx_entry {
cista_rtree::coord_t min, max;
uint32_t data;
bool operator==(ctx_entry other) const{
return cista_rtree::rect::coord_t_equal(this->min, other.min) && cista_rtree::rect::coord_t_equal(this->max, other.max) && this->data == other.data;
bool operator==(ctx_entry other) const {
return cista_rtree::rect::coord_t_equal(this->min, other.min) &&
cista_rtree::rect::coord_t_equal(this->max, other.max) &&
this->data == other.data;
}
};

// Struct for comparing found entries across all rtrees
struct iter_ref_ctx {
size_t count;
uint32_t expected_value;
Expand All @@ -33,16 +34,21 @@ struct iter_ref_ctx {
std::vector<ctx_entry> found_entries_mm;
};

bool iter_ref(const double *min, const double *max, const void *data,
void *udata)
{
auto *ctx = static_cast<iter_ref_ctx*>(udata);
// Comparator handled by the C implementation of the rtree
#pragma clang diagnostic push
#pragma ide diagnostic ignored "ConstantFunctionResult"
bool iter_ref(const double* min, const double* max, const void* data,
void* udata) {
auto* ctx = static_cast<iter_ref_ctx*>(udata);
auto input_data = static_cast<uint32_t>(reinterpret_cast<uint64_t>(data));
ctx_entry search_entry{.min = {static_cast<float>(min[0]), static_cast<float>(min[1])}, .max = {static_cast<float>(max[0]), static_cast<float>(max[1])}, .data = input_data};
ctx_entry search_entry{
.min = {static_cast<float>(min[0]), static_cast<float>(min[1])},
.max = {static_cast<float>(max[0]), static_cast<float>(max[1])},
.data = input_data};

for (auto & found_entrie : ctx->found_entries) {
for (auto& found_entrie : ctx->found_entries) {
if (found_entrie == search_entry) {
for (auto & found_entrie_mm : ctx->found_entries_mm) {
for (auto& found_entrie_mm : ctx->found_entries_mm) {
if (found_entrie_mm == search_entry) {
ctx->count++;
return true;
Expand All @@ -52,8 +58,14 @@ bool iter_ref(const double *min, const double *max, const void *data,
}
return true;
}


#pragma clang diagnostic pop

/**
* Test bench for the Fuzzer
* @param data Array of bytes used as input and commands for the rtrees
* @param size The size of the data Array
* @return non-zero if there is a discrepancy across the rtrees
*/
int test_bench(uint8_t const* data, size_t size) {

/**
Expand All @@ -62,7 +74,7 @@ int test_bench(uint8_t const* data, size_t size) {
* b8 - 135: 4x 32bit float for rects [min_0, max_0, min_1, max_1]
* b136 - b168: int data
*/
// Add memory dump fuzzing
// Add memory dump fuzzing

enum operator_ {
SEARCH = 0,
Expand All @@ -71,21 +83,43 @@ int test_bench(uint8_t const* data, size_t size) {
SAVE_LOAD = 3,
};

auto f = cista::mmap{"./mmap_rtree_nodes.bin", cista::mmap::protection::WRITE};

// mmap used by the memory mapped rtree
auto f =
cista::mmap{"./mmap_rtree_nodes.bin", cista::mmap::protection::WRITE};

// The reference implementation in C
auto ref_tree = rtree_new_with_allocator(malloc, free);
// The implementation to test
cista_rtree uut_tree;
mm_rtree cista_mm_rtree{mm_rtree::rect(), mm_rtree::node_idx_t::invalid(), mm_rtree::node_idx_t::invalid(), 0, 0, {}, cista::mmap_vec_map<mm_rtree::node_idx_t, mm_rtree::node>{std::move(f)}};

// A memory mapped version of the implementation to test
mm_rtree cista_mm_rtree{
mm_rtree::rect(),
mm_rtree::node_idx_t::invalid(),
mm_rtree::node_idx_t::invalid(),
0,
0,
{},
cista::mmap_vec_map<mm_rtree::node_idx_t, mm_rtree::node>{std::move(f)}};

for (size_t current_position = 0; current_position + 21 < size;) {
// Extracting the current command
uint8_t op = data[current_position] >> 6;
uint8_t min_0[4] = {data[current_position + 1], data[current_position + 2], data[current_position + 3], data[current_position + 4]};
uint8_t min_1[4] = {data[current_position + 5], data[current_position + 6], data[current_position + 7], data[current_position + 8]};
uint8_t max_0[4] = {data[current_position + 9], data[current_position + 10], data[current_position + 11], data[current_position + 12]};
uint8_t max_1[4] = {data[current_position + 13], data[current_position + 14], data[current_position + 15], data[current_position + 16]};
uint32_t input_data = data[current_position + 17] + (data[current_position + 18] << 8) + (data[current_position + 19] << 16) + (data[current_position + 20] << 24);
// Extracting the current coordinates
uint8_t min_0[4] = {data[current_position + 1], data[current_position + 2],
data[current_position + 3], data[current_position + 4]};
uint8_t min_1[4] = {data[current_position + 5], data[current_position + 6],
data[current_position + 7], data[current_position + 8]};
uint8_t max_0[4] = {data[current_position + 9], data[current_position + 10],
data[current_position + 11],
data[current_position + 12]};
uint8_t max_1[4] = {
data[current_position + 13], data[current_position + 14],
data[current_position + 15], data[current_position + 16]};
// Extracting the payload data
uint32_t input_data = data[current_position + 17] +
(data[current_position + 18] << 8) +
(data[current_position + 19] << 16) +
(data[current_position + 20] << 24);
uint32_t min_0u, max_0u, min_1u, max_1u;

memcpy(&min_0u, &min_0, sizeof(float));
Expand All @@ -94,7 +128,7 @@ int test_bench(uint8_t const* data, size_t size) {
memcpy(&max_1u, &max_1, sizeof(float));

float min_0f = static_cast<float>(static_cast<double>(min_0u) / 65536);
float max_0f = static_cast<float>(static_cast<double >(max_0u) / 65536);
float max_0f = static_cast<float>(static_cast<double>(max_0u) / 65536);
float min_1f = static_cast<float>(static_cast<double>(min_1u) / 65536);
float max_1f = static_cast<float>(static_cast<double>(max_1u) / 65536);

Expand All @@ -113,47 +147,65 @@ int test_bench(uint8_t const* data, size_t size) {
iter_ref_ctx ctx{};
ctx.count = 0;
ctx.expected_value = 0;
uut_tree.search(coord_min, coord_max, [coord_min, coord_max, &ctx](cista_rtree::coord_t const& min_temp, cista_rtree::coord_t const& max_temp, uint32_t data){
if (cista_rtree::rect::coord_t_equal(coord_min, min_temp) && cista_rtree::rect::coord_t_equal(coord_max, max_temp)) {
ctx.expected_value++;
ctx_entry input_entry{};
input_entry.min = min_temp;
input_entry.max = max_temp;
input_entry.data = data;
ctx.found_entries.emplace_back(input_entry);
}
return true;
});
uut_tree.search(
coord_min, coord_max,
[coord_min, coord_max, &ctx](cista_rtree::coord_t const& min_temp,
cista_rtree::coord_t const& max_temp,
uint32_t data) {
if (cista_rtree::rect::coord_t_equal(coord_min, min_temp) &&
cista_rtree::rect::coord_t_equal(coord_max, max_temp)) {
ctx.expected_value++;
ctx_entry input_entry{};
input_entry.min = min_temp;
input_entry.max = max_temp;
input_entry.data = data;
ctx.found_entries.emplace_back(input_entry);
}
return true;
});

ctx.expected_value_mm = 0;
cista_mm_rtree.search(coord_min, coord_max, [coord_min, coord_max, &ctx](cista_rtree::coord_t const& min_temp, cista_rtree::coord_t const& max_temp, uint32_t data){
if (cista_rtree::rect::coord_t_equal(coord_min, min_temp) && cista_rtree::rect::coord_t_equal(coord_max, max_temp)) {
ctx.expected_value_mm++;
ctx_entry input_entry{};
input_entry.min = min_temp;
input_entry.max = max_temp;
input_entry.data = data;
ctx.found_entries_mm.emplace_back(input_entry);
}
return true;
});
cista_mm_rtree.search(
coord_min, coord_max,
[coord_min, coord_max, &ctx](cista_rtree::coord_t const& min_temp,
cista_rtree::coord_t const& max_temp,
uint32_t data) {
if (cista_rtree::rect::coord_t_equal(coord_min, min_temp) &&
cista_rtree::rect::coord_t_equal(coord_max, max_temp)) {
ctx.expected_value_mm++;
ctx_entry input_entry{};
input_entry.min = min_temp;
input_entry.max = max_temp;
input_entry.data = data;
ctx.found_entries_mm.emplace_back(input_entry);
}
return true;
});

rtree_search(ref_tree, rect_min, rect_max, iter_ref, &ctx);

if (ctx.count != ctx.expected_value || ctx.count != ctx.expected_value_mm || ctx.expected_value != ctx.expected_value_mm) {
if (ctx.count != ctx.expected_value ||
ctx.count != ctx.expected_value_mm ||
ctx.expected_value != ctx.expected_value_mm) {
rtree_free(ref_tree);
abort();
}
}

if (op == INSERT) {
uut_tree.insert(coord_min, coord_max, input_data);
cista_mm_rtree.insert(coord_min, coord_max, input_data);
rtree_insert(ref_tree, rect_min, rect_max,reinterpret_cast<uintptr_t*>(static_cast<uint64_t>(input_data)));
rtree_insert(
ref_tree, rect_min, rect_max,
reinterpret_cast<uintptr_t*>(static_cast<uint64_t>(input_data)));
}

if (op == DELETE) {
uut_tree.delete_element(coord_min, coord_max, input_data);
cista_mm_rtree.delete_element(coord_min, coord_max, input_data);
rtree_delete(ref_tree, rect_min, rect_max, reinterpret_cast<uintptr_t*>(static_cast<uint64_t>(input_data)));
rtree_delete(
ref_tree, rect_min, rect_max,
reinterpret_cast<uintptr_t*>(static_cast<uint64_t>(input_data)));
}

if (op == SAVE_LOAD) {
Expand All @@ -162,8 +214,11 @@ int test_bench(uint8_t const* data, size_t size) {
cista_mm_rtree.write_header_bin(file);
file.close();

auto save_load_file = cista::mmap{"./mmap_rtree_nodes.bin", cista::mmap::protection::MODIFY};
cista_mm_rtree.nodes_ = cista::mmap_vec_map<mm_rtree::node_idx_t, mm_rtree::node>{std::move(save_load_file)};
auto save_load_file = cista::mmap{"./mmap_rtree_nodes.bin",
cista::mmap::protection::MODIFY};
cista_mm_rtree.nodes_ =
cista::mmap_vec_map<mm_rtree::node_idx_t, mm_rtree::node>{
std::move(save_load_file)};

file.open("mmap_rtree_header.bin", std::ios::binary | std::ios::in);
cista_mm_rtree.read_header_bin(file);
Expand All @@ -177,8 +232,6 @@ int test_bench(uint8_t const* data, size_t size) {
return 0;
}



#if defined(GENERATE_SEED)
int main() {}
#elif defined(MAIN)
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