This PR introduces several performance optimizations for the binary write/build process

- it changes the way how the number of symbols is reduced and how offsets to names are calculated.
  Instead of n^2 algorithms, it introduces nlog(n) algorithm.
  When the symbols optimization step is performed map<symbol_name, offset_to_name>
  is created so it saves another n^2 pass
- a couple of performance improvements to filter_iterator - from pre to post incrementation
  to save an unneeded copy, memoization of end iterator as the compiler cannot do it on its own
  and recreates it every loop iteration, simplified construction of the end iterator
  on the test binary that has a couple of hundreds of MB, it reduces the execution time of
  elf_add_section example form 20 minutes to a couple of seconds
- adds an ability to modify single value inplace in the sectiton to save coying it just to do that
- the reason behind this patch is to use LIEF as a patchelf replacement so the performance
  is one of the factors

Signed-off-by: Janusz Lisiecki <jlisiecki@nvidia.com>

include/LIEF/ELF/Builder.hpp

@@ -1,5 +1,6 @@
 /* Copyright 2017 R. Thomas
  * Copyright 2017 Quarkslab
+ * Copyright 2020, NVIDIA CORPORATION. All rights reserved
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -20,6 +21,7 @@
 #include <memory>
 #include <algorithm>
 #include <string>
+#include <unordered_map>
 
 #include "LIEF/visibility.h"
 #include "LIEF/iostream.hpp"
@@ -96,7 +98,8 @@ class LIEF_API Builder {
     void build_symbol_definition(void);
 
     template<typename T, typename HANDLER>
-    std::vector<std::string> optimize(const HANDLER& e);
+    std::vector<std::string> optimize(const HANDLER& e,
+                                      std::unordered_map<std::string, size_t> *of_map_p=nullptr);
 
     template<typename ELF_T>
     void build_symbol_version(void);

include/LIEF/ELF/Segment.hpp

@@ -81,6 +81,9 @@ class LIEF_API Segment : public Object {
     void alignment(uint64_t alignment);
     void content(const std::vector<uint8_t>& content);
     void content(std::vector<uint8_t>&& content);
+    template<typename T> T get_content_value(size_t offset) const;
+    template<typename T> void set_content_value(size_t offset, T value);
+    size_t get_content_size() const;
 
     it_sections       sections(void);
     it_const_sections sections(void) const;

include/LIEF/iterators.hpp

@@ -1,5 +1,6 @@
 /* Copyright 2017 R. Thomas
  * Copyright 2017 Quarkslab
+ * Copyright 2020, NVIDIA CORPORATION. All rights reserved.
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -367,7 +368,8 @@ class filter_iterator : public std::iterator<
   }
 
   filter_iterator end(void) const {
-    filter_iterator it_end{this->container_, this->filters_};
+    // we don't need filter for the end iterator
+    filter_iterator it_end{this->container_};
 
     it_end.it_       =  it_end.container_.end();
     it_end.distance_ = it_end.container_.size();
@@ -432,7 +434,8 @@ class filter_iterator : public std::iterator<
     filter_iterator it = this->begin();
     size_t size = 0;
 
-    while (it++ != std::end(it)) size++;
+    auto end_iter = std::end(it);
+    for (; it != end_iter; ++it) ++size;
     this->size_c_ = size;
     return this->size_c_;
   }

src/ELF/Binary.tcc

@@ -234,8 +234,8 @@ void Binary::patch_addend(Relocation& relocation, uint64_t from, uint64_t shift)
   VLOG(VDEBUG) << "Patch addend relocation at address: 0x" << std::hex << address;
   Segment& segment = segment_from_virtual_address(address);
   const uint64_t relative_offset = this->virtual_address_to_offset(address) - segment.file_offset();
-  std::vector<uint8_t> segment_content = segment.content();
-  const size_t segment_size = segment_content.size();
+
+  const size_t segment_size = segment.get_content_size();
 
   if (segment_size == 0) {
     LOG(WARNING) << "Segment is empty nothing to do";
@@ -247,13 +247,13 @@ void Binary::patch_addend(Relocation& relocation, uint64_t from, uint64_t shift)
     return;
   }
 
-  T* value = reinterpret_cast<T*>(segment_content.data() + relative_offset);
+  T value = segment.get_content_value<T>(relative_offset);
 
-  if (value != nullptr and *value >= from) {
-    *value += shift;
+  if (value >= from) {
+    value += shift;
   }
 
-  segment.content(segment_content);
+  segment.set_content_value(relative_offset, value);
 }
 
 

src/ELF/Builder.tcc

@@ -1,5 +1,6 @@
 /* Copyright 2017 R. Thomas
  * Copyright 2017 Quarkslab
+ * Copyright 2020, NVIDIA CORPORATION. All rights reserved.
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -14,6 +15,7 @@
  * limitations under the License.
  */
 #include <numeric>
+#include <unordered_map>
 
 #include "LIEF/logging++.hpp"
 
@@ -144,15 +146,16 @@ void Builder::build(void) {
 
 }
 
-
 template<typename T, typename HANDLER>
-std::vector<std::string> Builder::optimize(const HANDLER& container) {
+std::vector<std::string> Builder::optimize(const HANDLER& container,
+                                           std::unordered_map<std::string, size_t> *of_map_p) {
 
   std::set<std::string> string_table;
-
   std::vector<std::string> string_table_optimized;
+  string_table_optimized.reserve(container.size());
 
-  // Insert all strings in a std::set<> ordered by size
+  // reverse all symbol names and sort them so we can merge then in the linear time:
+  // aaa, aadd, aaaa, cca, ca -> aaaa, aaa, acc, ac ddaa
   std::transform(
     std::begin(container),
     std::end(container),
@@ -161,32 +164,73 @@ std::vector<std::string> Builder::optimize(const HANDLER& container) {
       std::end(string_table)),
     std::mem_fn(static_cast<const std::string& (T::*)(void) const>(&T::name)));
 
-  std::vector<std::string> sorted_table;
-  sorted_table.reserve(container.size());
-  std::move(std::begin(string_table), std::end(string_table),
-      std::back_inserter(sorted_table));
+  for (auto &val: string_table) {
+    string_table_optimized.emplace_back(std::move(val));
+    std::reverse(std::begin(string_table_optimized.back()), std::end(string_table_optimized.back()));
+  }
 
-  std::stable_sort(std::begin(sorted_table), std::end(sorted_table),
-    [] (const std::string& lhs, const std::string& rhs) {
-      return lhs.size() >= rhs.size();
-    });
-
-  // Optimize the string table
-  std::copy_if(
-    std::begin(sorted_table),
-    std::end(sorted_table),
-    std::back_inserter(string_table_optimized),
-    [&string_table_optimized] (const std::string& name) {
-      // Check if the given string **IS** the suffix of another string
-      auto it = std::find_if(
-          std::begin(string_table_optimized),
-          std::end(string_table_optimized),
-          [&name] (const std::string& nameOpti) {
-            return nameOpti.substr(nameOpti.size() - name.size()) == name ;
-          });
-      return (it == std::end(string_table_optimized));
+  std::sort(std::begin(string_table_optimized), std::end(string_table_optimized),
+      [] (const std::string& lhs, const std::string& rhs) {
+          bool ret = false;
+          if (lhs.size() > rhs.size()) {
+              auto res = lhs.compare(0, rhs.size(), rhs);
+              ret = (res <= 0);
+          } else {
+              auto res = rhs.compare(0, lhs.size(), lhs);
+              ret = (res > 0);
+          }
+          return ret;
   });
 
+  // as all elements that can be merged are adjacent we can just go through the list once
+  // and memorize one we merged to calculate the offsets later
+  std::unordered_map<std::string, std::string> merged_map;
+  size_t to_set_idx = 0, cur_elm_idx = 1;
+  for (; cur_elm_idx < string_table_optimized.size(); ++cur_elm_idx) {
+      auto &cur_elm = string_table_optimized[cur_elm_idx];
+      auto &to_set_elm = string_table_optimized[to_set_idx];
+      if (to_set_elm.size() >= cur_elm.size()) {
+          auto ret = to_set_elm.compare(0, cur_elm.size(), cur_elm);
+          if (ret == 0) {
+              // when memorizing reverse back symbol names
+              std::string rev_cur_elm = cur_elm;
+              std::string rev_to_set_elm = to_set_elm;
+              std::reverse(std::begin(rev_cur_elm), std::end(rev_cur_elm));
+              std::reverse(std::begin(rev_to_set_elm), std::end(rev_to_set_elm));
+              merged_map[rev_cur_elm] = rev_to_set_elm;
+              continue;
+          }
+      }
+      ++to_set_idx;
+      std::swap(string_table_optimized[to_set_idx], cur_elm);
+  }
+  // if the first one is empty
+  if (string_table_optimized[0].size() == 0) {
+    std::swap(string_table_optimized[0], string_table_optimized[to_set_idx]);
+    --to_set_idx;
+  }
+  string_table_optimized.resize(to_set_idx + 1);
+
+  //reverse symbols back and sort them again
+  for (auto &val: string_table_optimized) {
+      std::reverse(std::begin(val), std::end(val));
+  }
+  std::sort(std::begin(string_table_optimized), std::end(string_table_optimized));
+
+  if (of_map_p) {
+    std::unordered_map<std::string, size_t> offset_map;
+    offset_map[""] = 0;
+    size_t offset_counter = 1;
+    for (const auto &v : string_table_optimized) {
+        offset_map[v] = offset_counter;
+        offset_counter += v.size() + 1;
+    }
+    for (const auto &kv : merged_map) {
+        offset_map[kv.first] = offset_map[kv.second] + (kv.second.size() - kv.first.size());
+    }
+    *of_map_p = std::move(offset_map);
+  }
+
   return string_table_optimized;
 }
 
@@ -442,10 +486,12 @@ void Builder::build_static_symbols(void) {
   vector_iostream content(this->should_swap());
   content.reserve(this->binary_->static_symbols_.size() * sizeof(Elf_Sym));
   std::vector<uint8_t> string_table_raw;
+  std::unordered_map<std::string, size_t> offset_name_map;
 
   // Container which will hold symbols name (optimized)
   std::vector<std::string> string_table_optimize =
-    this->optimize<Symbol, decltype(this->binary_->static_symbols_)>(this->binary_->static_symbols_);
+    this->optimize<Symbol, decltype(this->binary_->static_symbols_)>(this->binary_->static_symbols_,
+                                                                     &offset_name_map);
 
   // We can't start with a symbol name
   string_table_raw.push_back(0);
@@ -459,19 +505,13 @@ void Builder::build_static_symbols(void) {
     VLOG(VDEBUG) << "Dealing with symbol: " << symbol->name();
     const std::string& name = symbol->name();
 
-    // Check if name is already pressent
-    auto&& it_name = std::search(
-        std::begin(string_table_raw),
-        std::end(string_table_raw),
-        name.c_str(),
-        name.c_str() + name.size() + 1);
-
-
-    if (it_name == std::end(string_table_raw)) {
-      throw LIEF::not_found("Unable to find symbol '" + name + "' in the string table");
+    auto offset_it = offset_name_map.find(name);
+    if (offset_it == std::end(offset_name_map)) {
+       throw LIEF::not_found("Unable to find symbol '" + name + "' in the string table");
     }
 
-    const Elf_Off name_offset = static_cast<Elf_Off>(std::distance(std::begin(string_table_raw), it_name));
+    const Elf_Off name_offset = static_cast<Elf_Off>(offset_it->second);
+
 
     Elf_Sym sym_hdr;
     memset(&sym_hdr, 0, sizeof(sym_hdr));
@@ -1052,33 +1092,29 @@ void Builder::build_dynamic_symbols(void) {
 
   // Build symbols string table
   std::vector<uint8_t> string_table_raw = string_table_section.content();
+  std::unordered_map<std::string, size_t> offset_name_map;
+  size_t additional_offset = string_table_raw.size() - 1;
 
   std::vector<std::string> string_table_optimized =
-    this->optimize<Symbol, decltype(this->binary_->dynamic_symbols_)>(this->binary_->dynamic_symbols_);
+    this->optimize<Symbol, decltype(this->binary_->dynamic_symbols_)>(this->binary_->dynamic_symbols_,
+                                    &offset_name_map);
 
   for (const std::string& name : string_table_optimized) {
     string_table_raw.insert(std::end(string_table_raw), std::begin(name), std::end(name));
     string_table_raw.push_back(0);
   }
 
-
   //
   // Build symbols
   //
   vector_iostream symbol_table_raw(this->should_swap());
   for (const Symbol* symbol : this->binary_->dynamic_symbols_) {
     const std::string& name = symbol->name();
-    // Check if name is already pressent
-    auto&& it_name = std::search(
-        std::begin(string_table_raw),
-        std::end(string_table_raw),
-        name.c_str(),
-        name.c_str() + name.size() + 1);
-
-    if (it_name == std::end(string_table_raw)) {
+    auto offset_it = offset_name_map.find(name);
+    if (offset_it == std::end(offset_name_map)) {
       throw LIEF::not_found("Unable to find the symbol in the string table");
     }
-    const Elf_Off name_offset = static_cast<Elf_Off>(std::distance(std::begin(string_table_raw), it_name));
+    const Elf_Off name_offset = static_cast<Elf_Off>(offset_name_map[name] + additional_offset);
 
     Elf_Sym sym_header;
 
@@ -1285,15 +1321,15 @@ void Builder::build_dynamic_relocations(void) {
   VLOG(VDEBUG) << "[+] Building dynamic relocations";
 
   it_dynamic_relocations dynamic_relocations = this->binary_->dynamic_relocations();
-
+  auto end_iter = std::end(dynamic_relocations);
   bool isRela = dynamic_relocations[0].is_rela();
-  if (not std::all_of(
-        std::begin(dynamic_relocations),
-        std::end(dynamic_relocations),
-        [isRela] (const Relocation& relocation) {
-          return relocation.is_rela() == isRela;
-        })) {
-      throw LIEF::type_error("Relocation are not of the same type");
+  for (; dynamic_relocations != end_iter; ++dynamic_relocations) {
+    if (dynamic_relocations->is_rela() != isRela) {
+      break;
+    }
+  }
+  if (dynamic_relocations != end_iter) {
+    throw LIEF::type_error("Relocation are not of the same type");
   }
 
   dynamic_entries_t::iterator it_dyn_relocation;

src/ELF/Segment.cpp

@@ -182,6 +182,62 @@ std::vector<uint8_t> Segment::content(void) const {
   return {binary_content.data() + node.offset(), binary_content.data() + node.offset() + node.size()};
 }
 
+size_t Segment::get_content_size() const {
+  DataHandler::Node& node = this->datahandler_->get(
+      this->file_offset(),
+      this->physical_size(),
+      DataHandler::Node::SEGMENT);
+  return node.size();
+}
+template<typename T> T Segment::get_content_value(size_t offset) const {
+  T ret;
+  if (this->datahandler_ == nullptr) {
+    VLOG(VDEBUG) << "Content from cache";
+    memcpy(&ret, this->content_c_.data() + offset, sizeof(T));
+  } else {
+    DataHandler::Node& node = this->datahandler_->get(
+        this->file_offset(),
+        this->physical_size(),
+        DataHandler::Node::SEGMENT);
+    const std::vector<uint8_t>& binary_content = this->datahandler_->content();
+    memcpy(&ret, binary_content.data() + node.offset() + offset, sizeof(T));
+  }
+  return ret;
+}
+
+template unsigned short Segment::get_content_value<unsigned short>(size_t offset) const;
+template unsigned int Segment::get_content_value<unsigned int>(size_t offset) const;
+template unsigned long Segment::get_content_value<unsigned long>(size_t offset) const;
+template unsigned long long Segment::get_content_value<unsigned long long>(size_t offset) const;
+
+template<typename T> void Segment::set_content_value(size_t offset, T value) {
+  if (this->datahandler_ == nullptr) {
+    VLOG(VDEBUG) << "Content from cache";
+    if (offset + sizeof(T) > this->content_c_.size()) {
+      this->content_c_.resize(offset + sizeof(T));
+      this->physical_size(offset + sizeof(T));
+    }
+    memcpy(this->content_c_.data() + offset, &value, sizeof(T));
+  } else {
+    DataHandler::Node& node = this->datahandler_->get(
+        this->file_offset(),
+        this->physical_size(),
+        DataHandler::Node::SEGMENT);
+    std::vector<uint8_t>& binary_content = this->datahandler_->content();
+
+    if (offset + sizeof(T) > binary_content.size()) {
+      this->datahandler_->reserve(node.offset(), offset + sizeof(T));
+      LOG(WARNING) << "You inserted data in segment '"
+                  << to_string(this->type()) << "' It may lead to overaly!" << std::endl;
+    }
+    this->physical_size(node.size());
+    memcpy(binary_content.data() + node.offset() + offset, &value, sizeof(T));
+  }
+}
+template void Segment::set_content_value<unsigned short>(size_t offset, unsigned short value);
+template void Segment::set_content_value<unsigned int>(size_t offset, unsigned int value);
+template void Segment::set_content_value<unsigned long>(size_t offset, unsigned long value);
+template void Segment::set_content_value<unsigned long long>(size_t offset, unsigned long long value);
 
 it_const_sections Segment::sections(void) const {
   return {this->sections_};