Merge branch 'master' of https://github.com/pauldb89/cdec

1 files changed, 548 insertions, 0 deletions

diff --git a/klm/util/stream/sort.hh b/klm/util/stream/sort.hh
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+++ b/klm/util/stream/sort.hh
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+/* Usage:
+ * Sort<Compare> sorter(temp, compare);
+ * Chain(config) >> Read(file) >> sorter.Unsorted();
+ * Stream stream;
+ * Chain chain(config) >> sorter.Sorted(internal_config, lazy_config) >> stream;
+ * 
+ * Note that sorter must outlive any threads that use Unsorted or Sorted.  
+ *
+ * Combiners take the form:
+ * bool operator()(void *into, const void *option, const Compare &compare) const
+ * which returns true iff a combination happened.  The sorting algorithm
+ * guarantees compare(into, option).  But it does not guarantee 
+ * compare(option, into).  
+ * Currently, combining is only done in merge steps, not during on-the-fly
+ * sort.  Use a hash table for that.  
+ */
+
+#ifndef UTIL_STREAM_SORT__
+#define UTIL_STREAM_SORT__
+
+#include "util/stream/chain.hh"
+#include "util/stream/config.hh"
+#include "util/stream/io.hh"
+#include "util/stream/stream.hh"
+#include "util/stream/timer.hh"
+
+#include "util/file.hh"
+#include "util/scoped.hh"
+#include "util/sized_iterator.hh"
+
+#include <algorithm>
+#include <iostream>
+#include <queue>
+#include <string>
+
+namespace util {
+namespace stream {
+
+struct NeverCombine {
+  template <class Compare> bool operator()(const void *, const void *, const Compare &) const { 
+    return false;
+  }
+};
+
+// Manage the offsets of sorted blocks in a file.  
+class Offsets {
+  public:
+    explicit Offsets(int fd) : log_(fd) {
+      Reset();
+    }
+
+    int File() const { return log_; }
+
+    void Append(uint64_t length) {
+      if (!length) return;
+      ++block_count_;
+      if (length == cur_.length) {
+        ++cur_.run;
+        return;
+      }
+      WriteOrThrow(log_, &cur_, sizeof(Entry));
+      cur_.length = length;
+      cur_.run = 1;
+    }
+
+    void FinishedAppending() {
+      WriteOrThrow(log_, &cur_, sizeof(Entry));
+      SeekOrThrow(log_, sizeof(Entry)); // Skip 0,0 at beginning.
+      cur_.run = 0;
+      if (block_count_) {
+        ReadOrThrow(log_, &cur_, sizeof(Entry));
+        assert(cur_.length);
+        assert(cur_.run);
+      }
+    }
+
+    uint64_t RemainingBlocks() const { return block_count_; }
+
+    uint64_t TotalOffset() const { return output_sum_; }
+
+    uint64_t PeekSize() const {
+      return cur_.length;
+    }
+
+    uint64_t NextSize() {
+      assert(block_count_);
+      uint64_t ret = cur_.length;
+      output_sum_ += ret;
+
+      --cur_.run;
+      --block_count_;
+      if (!cur_.run && block_count_) {
+        ReadOrThrow(log_, &cur_, sizeof(Entry));
+        assert(cur_.length);
+        assert(cur_.run);
+      }
+      return ret;
+    }
+
+    void Reset() {
+      SeekOrThrow(log_, 0);
+      ResizeOrThrow(log_, 0);
+      cur_.length = 0;
+      cur_.run = 0;
+      block_count_ = 0;
+      output_sum_ = 0;
+    }
+
+  private:
+    int log_;
+
+    struct Entry {
+      uint64_t length;
+      uint64_t run;
+    };
+    Entry cur_;
+
+    uint64_t block_count_;
+
+    uint64_t output_sum_;
+};
+
+// A priority queue of entries backed by file buffers
+template <class Compare> class MergeQueue {
+  public:
+    MergeQueue(int fd, std::size_t buffer_size, std::size_t entry_size, const Compare &compare)
+      : queue_(Greater(compare)), in_(fd), buffer_size_(buffer_size), entry_size_(entry_size) {}
+
+    void Push(void *base, uint64_t offset, uint64_t amount) {
+      queue_.push(Entry(base, in_, offset, amount, buffer_size_));
+    }
+
+    const void *Top() const {
+      return queue_.top().Current();
+    }
+
+    void Pop() {
+      Entry top(queue_.top());
+      queue_.pop();
+      if (top.Increment(in_, buffer_size_, entry_size_))
+        queue_.push(top);
+    }
+
+    std::size_t Size() const {
+      return queue_.size();
+    }
+
+    bool Empty() const {
+      return queue_.empty();
+    }
+
+  private:
+    // Priority queue contains these entries.  
+    class Entry {
+      public:
+        Entry() {}
+
+        Entry(void *base, int fd, uint64_t offset, uint64_t amount, std::size_t buf_size) {
+          offset_ = offset;
+          remaining_ = amount;
+          buffer_end_ = static_cast<uint8_t*>(base) + buf_size;
+          Read(fd, buf_size);
+        }
+
+        bool Increment(int fd, std::size_t buf_size, std::size_t entry_size) {
+          current_ += entry_size;
+          if (current_ != buffer_end_) return true;
+          return Read(fd, buf_size);
+        }
+
+        const void *Current() const { return current_; }
+
+      private:
+        bool Read(int fd, std::size_t buf_size) {
+          current_ = buffer_end_ - buf_size;
+          std::size_t amount;
+          if (static_cast<uint64_t>(buf_size) < remaining_) {
+            amount = buf_size;
+          } else if (!remaining_) {
+            return false;
+          } else {
+            amount = remaining_;
+            buffer_end_ = current_ + remaining_;
+          }
+          PReadOrThrow(fd, current_, amount, offset_);
+          offset_ += amount;
+          assert(current_ <= buffer_end_);
+          remaining_ -= amount;
+          return true;
+        }
+
+        // Buffer
+        uint8_t *current_, *buffer_end_;
+        // File
+        uint64_t remaining_, offset_;
+    };
+
+    // Wrapper comparison function for queue entries.   
+    class Greater : public std::binary_function<const Entry &, const Entry &, bool> {
+      public:
+        explicit Greater(const Compare &compare) : compare_(compare) {}
+
+        bool operator()(const Entry &first, const Entry &second) const {
+          return compare_(second.Current(), first.Current());
+        }
+
+      private:
+        const Compare compare_;
+    };
+
+    typedef std::priority_queue<Entry, std::vector<Entry>, Greater> Queue;
+    Queue queue_;
+
+    const int in_;
+    const std::size_t buffer_size_;
+    const std::size_t entry_size_;
+};
+
+/* A worker object that merges.  If the number of pieces to merge exceeds the
+ * arity, it outputs multiple sorted blocks, recording to out_offsets.  
+ * However, users will only every see a single sorted block out output because
+ * Sort::Sorted insures the arity is higher than the number of pieces before
+ * returning this.   
+ */
+template <class Compare, class Combine> class MergingReader {
+  public:
+    MergingReader(int in, Offsets *in_offsets, Offsets *out_offsets, std::size_t buffer_size, std::size_t total_memory, const Compare &compare, const Combine &combine) :
+        compare_(compare), combine_(combine),
+        in_(in),
+        in_offsets_(in_offsets), out_offsets_(out_offsets),
+        buffer_size_(buffer_size), total_memory_(total_memory) {}
+
+    void Run(const ChainPosition &position) {
+      Run(position, false);
+    }
+
+    void Run(const ChainPosition &position, bool assert_one) {
+      // Special case: nothing to read.  
+      if (!in_offsets_->RemainingBlocks()) {
+        Link l(position);
+        l.Poison();
+        return;
+      }
+      // If there's just one entry, just read.
+      if (in_offsets_->RemainingBlocks() == 1) {
+        // Sequencing is important.
+        uint64_t offset = in_offsets_->TotalOffset();
+        uint64_t amount = in_offsets_->NextSize();
+        ReadSingle(offset, amount, position);
+        if (out_offsets_) out_offsets_->Append(amount);
+        return;
+      }
+
+      Stream str(position);
+      scoped_malloc buffer(MallocOrThrow(total_memory_));
+      uint8_t *const buffer_end = static_cast<uint8_t*>(buffer.get()) + total_memory_;
+
+      const std::size_t entry_size = position.GetChain().EntrySize();
+
+      while (in_offsets_->RemainingBlocks()) {
+        // Use bigger buffers if there's less remaining.
+        uint64_t per_buffer = static_cast<uint64_t>(std::max<std::size_t>(
+            buffer_size_,
+            static_cast<std::size_t>((static_cast<uint64_t>(total_memory_) / in_offsets_->RemainingBlocks()))));
+        per_buffer -= per_buffer % entry_size;
+        assert(per_buffer);
+
+        // Populate queue.
+        MergeQueue<Compare> queue(in_, per_buffer, entry_size, compare_);
+        for (uint8_t *buf = static_cast<uint8_t*>(buffer.get()); 
+            in_offsets_->RemainingBlocks() && (buf + std::min(per_buffer, in_offsets_->PeekSize()) <= buffer_end);) {
+          uint64_t offset = in_offsets_->TotalOffset();
+          uint64_t size = in_offsets_->NextSize();
+          queue.Push(buf, offset, size);
+          buf += static_cast<std::size_t>(std::min<uint64_t>(size, per_buffer));
+        }
+        // This shouldn't happen but it's probably better to die than loop indefinitely.
+        if (queue.Size() < 2 && in_offsets_->RemainingBlocks()) {
+          std::cerr << "Bug in sort implementation: not merging at least two stripes." << std::endl;
+          abort();
+        }
+        if (assert_one && in_offsets_->RemainingBlocks()) {
+          std::cerr << "Bug in sort implementation: should only be one merge group for lazy sort" << std::endl;
+          abort();
+        }
+
+        uint64_t written = 0;
+        // Merge including combiner support.  
+        memcpy(str.Get(), queue.Top(), entry_size);
+        for (queue.Pop(); !queue.Empty(); queue.Pop()) {
+          if (!combine_(str.Get(), queue.Top(), compare_)) {
+            ++written; ++str;
+            memcpy(str.Get(), queue.Top(), entry_size);
+          }
+        }
+        ++written; ++str;
+        if (out_offsets_)
+          out_offsets_->Append(written * entry_size);
+      }
+      str.Poison();
+    }
+
+  private: 
+    void ReadSingle(uint64_t offset, const uint64_t size, const ChainPosition &position) {
+      // Special case: only one to read.  
+      const uint64_t end = offset + size;
+      const uint64_t block_size = position.GetChain().BlockSize();
+      Link l(position);
+      for (; offset + block_size < end; ++l, offset += block_size) {
+        PReadOrThrow(in_, l->Get(), block_size, offset);
+        l->SetValidSize(block_size);
+      }
+      PReadOrThrow(in_, l->Get(), end - offset, offset);
+      l->SetValidSize(end - offset);
+      (++l).Poison();
+      return;
+    }
+   
+    Compare compare_;
+    Combine combine_;
+
+    int in_;
+
+  protected:
+    Offsets *in_offsets_;
+
+  private:
+    Offsets *out_offsets_;
+ 
+    std::size_t buffer_size_;
+    std::size_t total_memory_;
+};
+
+// The lazy step owns the remaining files.  This keeps track of them.  
+template <class Compare, class Combine> class OwningMergingReader : public MergingReader<Compare, Combine> {
+  private:
+    typedef MergingReader<Compare, Combine> P;
+  public:
+    OwningMergingReader(int data, const Offsets &offsets, std::size_t buffer, std::size_t lazy, const Compare &compare, const Combine &combine) 
+      : P(data, NULL, NULL, buffer, lazy, compare, combine),
+        data_(data),
+        offsets_(offsets) {}
+
+    void Run(const ChainPosition &position) {
+      P::in_offsets_ = &offsets_;
+      scoped_fd data(data_);
+      scoped_fd offsets_file(offsets_.File());
+      P::Run(position, true);
+    }
+
+  private:
+    int data_;
+    Offsets offsets_;
+};
+
+// Don't use this directly.  Worker that sorts blocks.   
+template <class Compare> class BlockSorter {
+  public:
+    BlockSorter(Offsets &offsets, const Compare &compare) :
+      offsets_(&offsets), compare_(compare) {}
+
+    void Run(const ChainPosition &position) {
+      const std::size_t entry_size = position.GetChain().EntrySize();
+      for (Link link(position); link; ++link) {
+        // Record the size of each block in a separate file.    
+        offsets_->Append(link->ValidSize());
+        void *end = static_cast<uint8_t*>(link->Get()) + link->ValidSize();
+#if defined(_WIN32) || defined(_WIN64)
+        std::stable_sort
+#else
+        std::sort
+#endif
+          (SizedIt(link->Get(), entry_size),
+           SizedIt(end, entry_size),
+           compare_);
+      }
+      offsets_->FinishedAppending();
+    }
+
+  private:
+    Offsets *offsets_;
+    SizedCompare<Compare> compare_;
+};
+
+class BadSortConfig : public Exception {
+  public:
+    BadSortConfig() throw() {}
+    ~BadSortConfig() throw() {}
+};
+
+template <class Compare, class Combine = NeverCombine> class Sort {
+  public:
+    Sort(Chain &in, const SortConfig &config, const Compare &compare = Compare(), const Combine &combine = Combine())
+      : config_(config),
+        data_(MakeTemp(config.temp_prefix)),
+        offsets_file_(MakeTemp(config.temp_prefix)), offsets_(offsets_file_.get()),
+        compare_(compare), combine_(combine),
+        entry_size_(in.EntrySize()) {
+      UTIL_THROW_IF(!entry_size_, BadSortConfig, "Sorting entries of size 0");
+      // Make buffer_size a multiple of the entry_size.  
+      config_.buffer_size -= config_.buffer_size % entry_size_;
+      UTIL_THROW_IF(!config_.buffer_size, BadSortConfig, "Sort buffer too small");
+      UTIL_THROW_IF(config_.total_memory < config_.buffer_size * 4, BadSortConfig, "Sorting memory " << config_.total_memory << " is too small for four buffers (two read and two write).");
+      in >> BlockSorter<Compare>(offsets_, compare_) >> WriteAndRecycle(data_.get());
+    }
+
+    uint64_t Size() const {
+      return SizeOrThrow(data_.get());
+    }
+
+    // Do merge sort, terminating when lazy merge could be done with the
+    // specified memory.  Return the minimum memory necessary to do lazy merge.
+    std::size_t Merge(std::size_t lazy_memory) {
+      if (offsets_.RemainingBlocks() <= 1) return 0;
+      const uint64_t lazy_arity = std::max<uint64_t>(1, lazy_memory / config_.buffer_size);
+      uint64_t size = Size();
+      /* No overflow because
+       * offsets_.RemainingBlocks() * config_.buffer_size <= lazy_memory ||
+       * size < lazy_memory
+       */
+      if (offsets_.RemainingBlocks() <= lazy_arity || size <= static_cast<uint64_t>(lazy_memory))
+        return std::min<std::size_t>(size, offsets_.RemainingBlocks() * config_.buffer_size);
+
+      scoped_fd data2(MakeTemp(config_.temp_prefix));
+      int fd_in = data_.get(), fd_out = data2.get();
+      scoped_fd offsets2_file(MakeTemp(config_.temp_prefix));
+      Offsets offsets2(offsets2_file.get());
+      Offsets *offsets_in = &offsets_, *offsets_out = &offsets2;
+
+      // Double buffered writing.  
+      ChainConfig chain_config;
+      chain_config.entry_size = entry_size_;
+      chain_config.block_count = 2;
+      chain_config.total_memory = config_.buffer_size * 2;
+      Chain chain(chain_config);
+
+      while (offsets_in->RemainingBlocks() > lazy_arity) {
+        if (size <= static_cast<uint64_t>(lazy_memory)) break;
+        std::size_t reading_memory = config_.total_memory - 2 * config_.buffer_size;
+        if (size < static_cast<uint64_t>(reading_memory)) {
+          reading_memory = static_cast<std::size_t>(size);
+        }
+        SeekOrThrow(fd_in, 0);
+        chain >>
+          MergingReader<Compare, Combine>(
+              fd_in,
+              offsets_in, offsets_out,
+              config_.buffer_size,
+              reading_memory,
+              compare_, combine_) >>
+          WriteAndRecycle(fd_out);
+        chain.Wait();
+        offsets_out->FinishedAppending();
+        ResizeOrThrow(fd_in, 0);
+        offsets_in->Reset();
+        std::swap(fd_in, fd_out);
+        std::swap(offsets_in, offsets_out);
+        size = SizeOrThrow(fd_in);
+      }
+
+      SeekOrThrow(fd_in, 0);
+      if (fd_in == data2.get()) {
+        data_.reset(data2.release());
+        offsets_file_.reset(offsets2_file.release());
+        offsets_ = offsets2;
+      }
+      if (offsets_.RemainingBlocks() <= 1) return 0;
+      // No overflow because the while loop exited.
+      return std::min(size, offsets_.RemainingBlocks() * static_cast<uint64_t>(config_.buffer_size));
+    }
+
+    // Output to chain, using this amount of memory, maximum, for lazy merge
+    // sort.  
+    void Output(Chain &out, std::size_t lazy_memory) {
+      Merge(lazy_memory);
+      out.SetProgressTarget(Size());
+      out >> OwningMergingReader<Compare, Combine>(data_.get(), offsets_, config_.buffer_size, lazy_memory, compare_, combine_);
+      data_.release();
+      offsets_file_.release();
+    }
+
+    /* If a pipeline step is reading sorted input and writing to a different
+     * sort order, then there's a trade-off between using RAM to read lazily
+     * (avoiding copying the file) and using RAM to increase block size and, 
+     * therefore, decrease the number of merge sort passes in the next
+     * iteration.  
+     * 
+     * Merge sort takes log_{arity}(pieces) passes.  Thus, each time the chain
+     * block size is multiplied by arity, the number of output passes decreases
+     * by one.  Up to a constant, then, log_{arity}(chain) is the number of
+     * passes saved.  Chain simply divides the memory evenly over all blocks.
+     * 
+     * Lazy sort saves this many passes (up to a constant)
+     *   log_{arity}((memory-lazy)/block_count) + 1
+     * Non-lazy sort saves this many passes (up to the same constant):
+     *   log_{arity}(memory/block_count)
+     * Add log_{arity}(block_count) to both:
+     *   log_{arity}(memory-lazy) + 1 versus log_{arity}(memory)
+     * Take arity to the power of both sizes (arity > 1)
+     *   (memory - lazy)*arity versus memory
+     * Solve for lazy
+     *   lazy = memory * (arity - 1) / arity
+     */
+    std::size_t DefaultLazy() {
+      float arity = static_cast<float>(config_.total_memory / config_.buffer_size);
+      return static_cast<std::size_t>(static_cast<float>(config_.total_memory) * (arity - 1.0) / arity);
+    }
+
+    // Same as Output with default lazy memory setting.
+    void Output(Chain &out) {
+      Output(out, DefaultLazy());
+    }
+
+    // Completely merge sort and transfer ownership to the caller.
+    int StealCompleted() {
+      // Merge all the way.
+      Merge(0);
+      SeekOrThrow(data_.get(), 0);
+      offsets_file_.reset();
+      return data_.release();
+    }
+
+  private:
+    SortConfig config_;
+
+    scoped_fd data_;
+
+    scoped_fd offsets_file_;
+    Offsets offsets_;
+
+    const Compare compare_;
+    const Combine combine_;
+    const std::size_t entry_size_;
+};
+
+// returns bytes to be read on demand.  
+template <class Compare, class Combine> uint64_t BlockingSort(Chain &chain, const SortConfig &config, const Compare &compare = Compare(), const Combine &combine = NeverCombine()) {
+  Sort<Compare, Combine> sorter(chain, config, compare, combine);
+  chain.Wait(true);
+  uint64_t size = sorter.Size();
+  sorter.Output(chain);
+  return size;
+}
+
+} // namespace stream
+} // namespace util
+
+#endif // UTIL_STREAM_SORT__