Implement merge pass - not yet tested

sortbin.cpp

@@ -51,6 +51,7 @@
 
 #include <algorithm>
 #include <iterator>
+#include <memory>
 #include <stdexcept>
 #include <string>
 #include <system_error>
@@ -70,6 +71,10 @@
 /* Default number of sorting threads. */
 #define DEFAULT_THREADS             1
 
+/* Align buffer sizes and I/O on this number of records.
+   For efficiency, I/O should be done in multiples of 4096 bytes. */
+#define TRANSFER_ALIGNMENT          4096
+
 
 namespace {  // anonymous namespace
 
@@ -400,18 +405,19 @@ public:
  * Read binary records from an input file with buffering.
  *
  * The input stream reads from a sequence of discontinuous, equally spaced
- * sections in the input file. All sections have the same size, except for
+ * blocks in the input file. All blocks have the same size, except for
- * the last section which may be shorter if it runs to the end of the file.
+ * the last block which may be shorter if it runs to the end of the file.
- * Each section contains a flat array of binary records.
+ * Each block contains a flat array of binary records.
  *
- * The input stream starts in the "end_of_stream" state.
+ * The input stream starts in the "empty" state.
- * The first call to "next_section()" enables reading records from the
+ * The first call to "next_block()" enables reading records from the
- * first input section. When the input stream reaches the end of the
+ * first input block. When the input stream reaches the end of the
- * current section, it again enters the "end_of_stream" state until
+ * current block, it again enters the "empty" state until the following
- * the next call to "next_section()".
+ * call to "next_block()".
  */
 class RecordInputStream
 {
+// TODO : double-buffering with delayed I/O via background thread
 public:
     /**
      * Construct a record input stream.
@@ -420,12 +426,12 @@ public:
      *
      * @param input_file    Input file where records read from.
      * @param record_size   Record size in bytes.
-     * @param section_offset  Offset in input file of first input section.
+     * @param start_offset  Offset in input file of first input section.
-     * @param section_size    Size of each input section in bytes.
+     * @param block_size    Size of each input block in bytes.
      *                      Must be a multiple of "record_size".
-     *                        The last input section may be shorter if it
+     *                      The last input block may be shorter if it runs
-     *                        runs to the end of the file.
+     *                      to the end of the file.
-     * @param section_stride  Distance between start of sections in bytes.
+     * @param block_stride  Distance between start of blocks in bytes.
      * @param buffer_size   Buffer size in bytes.
      *                      Must be a multiple of "record_size".
      *                      Note: Each RecordInputStream creates two buffers
@@ -434,24 +440,24 @@ public:
     RecordInputStream(
         BinaryFile&   input_file,
         unsigned int  record_size,
-        uint64_t      section_offset,
+        uint64_t      start_offset,
-        uint64_t      section_size,
+        uint64_t      block_size,
-        uint64_t      section_stride,
+        uint64_t      block_stride,
         size_t        buffer_size)
       : m_input_file(input_file),
         m_record_size(record_size),
-        m_section_offset(section_offset),
+        m_block_offset(start_offset),
-        m_section_size(section_size),
+        m_block_size(block_size),
-        m_section_stride(section_stride),
+        m_block_stride(block_stride),
-        m_section_remaining(0),
+        m_block_remaining(0),
         m_file_offset(0),
         m_bufpos(NULL),
         m_bufend(NULL),
         m_buffer(buffer_size)
     {
-        assert(section_size % record_size == 0);
+        assert(start_offset <= input_file.size());
-        assert(section_size > record_size);
+        assert(block_size % record_size == 0);
-        assert(section_size <= section_stride);
+        assert(block_size <= block_stride);
         assert(buffer_size % record_size == 0);
         assert(buffer_size > record_size);
     }
@@ -460,8 +466,8 @@ public:
     RecordInputStream(const RecordInputStream&) = delete;
     RecordInputStream& operator=(const RecordInputStream&) = delete;
 
-    /** Return true if the end of the current input section is reached. */
+    /** Return true if the end of the current input block is reached. */
-    inline bool end_of_stream() const
+    inline bool empty() const
     {
         return (m_bufpos == m_bufend);
     }
@@ -472,7 +478,7 @@ public:
      * This function must only be used if "end_of_stream()" returns false.
      * The returned pointer becomes invalid after a call to "next_record()".
      */
-    inline const unsigned char * current_record() const
+    inline const unsigned char * record() const
     {
         return m_bufpos;
     }
@@ -480,7 +486,7 @@ public:
     /**
      * Move to the next record of the current section.
      *
-     * This function must only be used if "end_of_stream()" returns false.
+     * This function must only be used if "empty()" returns false.
      * Calling this function invalidates all pointers previously returned
      * by "current_record()".
      */
@@ -499,19 +505,19 @@ public:
     /**
      * Start reading from the next input section.
      *
-     * This function may only be called if "end_of_stream()" returns true.
+     * This function may only be called if "empty()" returns true.
      */
-    void next_section()
+    void next_block()
     {
         assert(m_bufpos == m_bufend);
 
         uint64_t file_size = m_input_file.size();
-        assert(m_section_stride < file_size - m_section_offset);
+        assert(m_block_stride < file_size - m_block_offset);
 
-        m_section_offset += m_section_stride;
+        m_block_offset += m_block_stride;
-        m_file_offset = m_section_offset;
+        m_file_offset = m_block_offset;
-        m_section_remaining =
+        m_block_remaining =
-            std::min(m_section_size, file_size - m_section_offset);
+            std::min(m_block_size, file_size - m_block_offset);
 
         refill_buffer();
     }
@@ -520,28 +526,27 @@ private:
     /** Refill the buffer from the current input section. */
     void refill_buffer()
     {
-        if (m_section_remaining > 0) {
+        if (m_block_remaining > 0) {
-            size_t block_size =
+            size_t transfer_size =
-                (m_buffer.size() < m_section_remaining) ?
+                (m_buffer.size() < m_block_remaining) ?
-                    m_buffer.size() : m_section_remaining;
+                    m_buffer.size() : m_block_remaining;
-            m_input_file.read(m_buffer.data(), m_file_offset, block_size);
+            m_input_file.read(m_buffer.data(), m_file_offset, transfer_size);
-            m_file_offset += block_size;
+            m_file_offset += transfer_size;
-            m_section_remaining -= block_size;
+            m_block_remaining -= transfer_size;
-            m_bufend = m_buffer.data() + block_size;
+            m_bufend = m_buffer.data() + transfer_size;
         }
     }
 
     BinaryFile&         m_input_file;
     const unsigned int  m_record_size;
-    uint64_t            m_section_offset;
+    uint64_t            m_block_offset;
-    uint64_t            m_section_size;
+    uint64_t            m_block_size;
-    uint64_t            m_section_stride;
+    uint64_t            m_block_stride;
-    uint64_t            m_section_remaining;
+    uint64_t            m_block_remaining;
     uint64_t            m_file_offset;
     unsigned char *     m_bufpos;
     unsigned char *     m_bufend;
     std::vector<unsigned char> m_buffer;
-// TODO : double-buffering with delayed I/O via background thread
 };
 
 
@@ -550,6 +555,7 @@ private:
  */
 class RecordOutputStream
 {
+// TODO : double-buffering with delayed I/O via background thread
 public:
     /**
      * Construct a record output stream.
@@ -602,7 +608,6 @@ private:
     uint64_t            m_file_offset;
     size_t              m_bufpos;
     std::vector<unsigned char>  m_buffer;
-// TODO : double-buffering with delayed I/O via background thread
 };
 
 
@@ -1212,6 +1217,147 @@ void sort_pass(
 }
 
 
+/**
+ * Merge 2 sorted blocks of records into a single sorted block.
+ *
+ * @param instream1         Input stream containing block 1.
+ * @param instream2         Input stream containing block 2.
+ * @param output_stream     Output stream for the merged block.
+ * @param record_size       Record size in bytes.
+ * @param filter_dupl       True to eliminate duplicate records.
+ */
+void merge_2_blocks(
+    RecordInputStream& instream1,
+    RecordInputStream& instream2,
+    RecordOutputStream& output_stream,
+    size_t record_size,
+    bool filter_dupl)
+{
+    // Merge until one stream runs empty.
+    if (!instream1.empty() && !instream2.empty()) {
+        const unsigned char * rec1 = instream1.record();
+        const unsigned char * rec2 = instream2.record();
+
+        while (true) {
+
+// TODO TODO : filter duplicates
+
+            // Choose which record should go first.
+            if (record_compare(rec1, rec2, record_size) < 0) {
+                // Push record from stream 1 and load next record.
+                output_stream.put(rec1);
+                instream1.next_record();
+                if (instream1.empty()) {
+                    break;
+                }
+                rec1 = instream1.record();
+            } else {
+                // Push record from stream 2 and load next record.
+                output_stream.put(rec2);
+                instream2.next_record();
+                if (instream2.empty()) {
+                    break;
+                }
+                rec2 = instream2.record();
+            }
+        }
+    }
+
+    // At most one of the streams still has records left.
+    // Copy those records to the output.
+
+    while (!instream1.empty()) {
+        output_stream.put(instream1.record());
+        instream1.next_record();
+    }
+
+    while (!instream2.empty()) {
+        output_stream.put(instream2.record());
+        instream2.next_record();
+    }
+}
+
+
+/**
+ * Merge sorted blocks of records into a single sorted block.
+ *
+ * @param input_streams     One input stream for each input blocks.
+ * @param output_stream     Output stream for the merged block.
+ * @param record_size       Record size in bytes.
+ * @param branch_factor     Number of input blocks.
+ *                          May be less than the length of input_streams.
+ * @param filter_dupl       True to eliminate duplicate records.
+ */
+void merge_n_blocks(
+    std::vector<std::unique_ptr<RecordInputStream>>& input_streams,
+    RecordOutputStream& output_stream,
+    size_t record_size,
+    unsigned int branch_factor,
+    bool filter_dupl)
+{
+    assert(branch_factor > 1);
+    assert(branch_factor <= input_streams.size());
+
+    // Put the head element of each block into a heap.
+    // The heap will determine which block contains the element that
+    // should go first in the merged block.
+    typedef std::tuple<const unsigned char*, RecordInputStream*> HeapElement;
+
+    // Function which compares records and returns true if
+    // record A comes after record B in sort order.
+    // If this function is used as the compare operator of a max-heap,
+    // the record that comes first in sort order will be at the top
+    // of the heap.
+    auto cmp_heap_elem =
+        [record_size](const HeapElement& a, const HeapElement& b) {
+            const unsigned char *reca = std::get<0>(a);
+            const unsigned char *recb = std::get<0>(b);
+            return record_compare(reca, recb, record_size) > 0;
+        };
+
+    // Initialize empty heap.
+    std::vector<HeapElement> heap;
+
+    // Get the first element of each block.
+    for (unsigned int i = 0; i < branch_factor; i++) {
+        if (!input_streams[i]->empty()) {
+            heap.emplace_back(input_streams[i]->record(),
+                              input_streams[i].get());
+        }
+    }
+
+    // Make a heap of the first blocks.
+    std::make_heap(heap.begin(), heap.end(), cmp_heap_elem);
+
+    // Keep merging until the heap runs empty.
+    while (!heap.empty()) {
+
+// TODO TODO : filter duplicates
+
+        // Extract the first element from the heap.
+        const unsigned char * rec;
+        RecordInputStream * instream;
+        std::tie(rec, instream) = heap[0];
+        std::pop_heap(heap.begin(), heap.end());
+
+        // Push this element to the output block.
+        output_stream.put(rec);
+
+        // Try to pull the next record from this input stream.
+        instream->next_record();
+        if (instream->empty()) {
+            // Stream is empty. This stream is now out of the game.
+            // The heap shrinks by 1 element.
+            heap.pop_back();
+        } else {
+            // Push next record from the stream into the heap.
+            heap.back() = std::make_tuple(instream->record(), instream);
+            std::push_heap(heap.begin(), heap.end());
+        }
+    }
+}
+
+
 /**
  * Perform a merge pass of multi-pass external sorting.
  *
@@ -1228,8 +1374,8 @@ void sort_pass(
  * @param output_file           Output file for this pass.
  * @param records_per_block     Number of records per input block.
  * @param num_blocks            Number of input blocks.
- * @param branch_factor         Number of blocks to merge per an output block.
+ * @param branch_factor         Number of blocks to merge per output block.
- * @param filter_duplicates     true to eliminate duplicate elements.
+ * @param filter_dupl           True to eliminate duplicate records.
  * @param ctx                   Reference to context structure.
  */
 void merge_pass(
@@ -1238,23 +1384,59 @@ void merge_pass(
     uint64_t records_per_block,
     uint64_t num_blocks,
     unsigned int branch_factor,
-    bool filter_duplicates,
+    bool filter_dupl,
     const SortContext& ctx)
 {
-// TODO TODO TODO TODO
+    assert(branch_factor > 1);
-#if 0
+    assert(branch_factor <= num_blocks);
-    // Eliminating duplicates is only supported for a single output block.
+
-    assert((!filter_duplicates) || (num_blocks <= branch_factor));
+    // Only filter duplicates when the output is a single block.
+    assert((!filter_dupl) || (branch_factor == num_blocks));
 
     Timer timer;
     timer.start();
 
-// TODO : double-buffer with I/O in separate thread
+    // Calculate number of buffers:
-    // Allocate sort buffer.
+    // 2 buffers per input stream + buffers for output 1 stream.
-    assert(records_per_block < SIZE_MAX / record_size);
+    size_t num_output_buffers = 2 + (branch_factor - 1) / 2;
-    std::vector<unsigned char> buffer(records_per_block * record_size);
+    size_t num_buffers = 2 * branch_factor + num_output_buffers;
+
+    // Calculate buffer size.
+    // Must be a multiple of the record size and the transfer alignment.
+    size_t buffer_size = ctx.memory_size / num_buffers;
+    buffer_size -= buffer_size % (TRANSFER_ALIGNMENT * ctx.record_size);
+
+// TODO : double-buffering with I/O in separate thread
+
+    // Initialize input streams.
+    std::vector<std::unique_ptr<RecordInputStream>> input_streams;
+    for (unsigned int i = 0; i < branch_factor; i++) {
+        uint64_t block_size = records_per_block * ctx.record_size;
+        uint64_t start_offset = i * block_size;
+        uint64_t block_stride = branch_factor * block_size;
+        if (start_offset >= input_file.size()) {
+            break;
+        }
+        input_streams.emplace_back(new RecordInputStream(
+            input_file,
+            ctx.record_size,
+            start_offset,
+            block_size,
+            block_stride,
+            buffer_size));
+    }
+
+    // Initialize output stream.
+    RecordOutputStream output_stream(
+        output_file,
+        ctx.record_size,
+        0,
+        buffer_size);
 
     // Loop over groups of blocks to be sorted.
+    // Every group consists of "branch_factor" blocks, except the last
+    // group which may contain fewer blocks.
+    // Each group produces one output block.
     uint64_t block_index = 0;
     while (block_index < num_blocks) {
 
@@ -1264,44 +1446,53 @@ void merge_pass(
             branch_factor = num_blocks - block_index;
         }
 
+        // Skip to the next section of each active input stream.
+        for (unsigned int i = 0; i < this_branch_factor; i++) {
+            input_streams[i]->next_block();
+        }
+
+        if (this_branch_factor == 1) {
+
+            // Last group contains just 1 block.
+            // Copy it to the output.
+            assert(!filter_dupl);
+            RecordInputStream * instream = input_streams[0].get();
+            while (!instream->empty()) {
+                output_stream.put(instream->record());
+                instream->next_record();
+            }
+
+        } else if (this_branch_factor == 2) {
+
+            // Special case for merging 2 blocks.
+            merge_2_blocks(
+                *input_streams[0],
+                *input_streams[1],
+                output_stream,
+                ctx.record_size,
+                filter_dupl);
+
+        } else {
+
+            // Merge more than 2 blocks.
+            merge_n_blocks(
+                input_streams,
+                output_stream,
+                ctx.record_size,
+                this_branch_factor,
+                filter_dupl);
 
         }
 
-    // Loop over blocks to be sorted.
+        // Skip to the start of the next block group.
-    for (uint64_t block_index = 0; block_index < num_blocks; block_index++) {
+        block_index += this_branch_factor;
-
-        uint64_t block_start_idx = block_index * records_per_block;
-        size_t block_num_records =
-            std::min(records_per_block, num_records - block_start_idx);
-
-        log(ctx,
-            "sorting block %" PRIu64 " / %" PRIu64 ": %" PRIu64 " records\n",
-            block_index,
-            num_blocks,
-            block_num_records);
-
-        // Read block.
-        input_file.read(
-            buffer.data(),
-            block_start_idx * record_size,
-            block_num_records * record_size);
-
-        // Sort records in this block.
-        sort_records(
-            buffer.data(),
-            record_size,
-            block_num_records);
-
-        // Write block.
-        output_file.write(
-            buffer.data(),
-            block_start_idx * record_size,
-            block_num_records * record_size);
     }
 
+    // Flush output stream buffers.
+    output_stream.flush();
+
     timer.stop();
     log(ctx, "  t = %.3f seconds\n", timer.value());
-#endif
 }
 
 
@@ -1313,17 +1504,16 @@ SortStrategy plan_multi_pass_strategy(
     const SortContext& ctx)
 {
     // Plan the initial sort pass.
-    // Use blocks that are at most half of available memory
+    // Use blocks that are at most half of available memory,
-    // (so we can use two buffers to overlap I/O and sorting).
+    // so we can use two buffers to overlap I/O and sorting.
     uint64_t max_sort_block_size = ctx.memory_size / 2;
 
     // Calculate number of records per block.
+    // Make sure this is a multiple of the transfer alignment size.
     uint64_t records_per_sort_block = max_sort_block_size / ctx.record_size;
+    records_per_sort_block -= records_per_sort_block % TRANSFER_ALIGNMENT;
 
-    // Make sure the block size is a multiple of 4096 bytes.
+    // Calculate number of blocks during the initial sort pass.
-    records_per_sort_block -= records_per_sort_block % 4096;
-
-    // Calculate the number of blocks during the initial sort pass.
     uint64_t num_records = file_size / ctx.record_size;
     uint64_t num_sort_blocks = 1 + (num_records - 1) / records_per_sort_block;
 
@@ -1374,7 +1564,8 @@ void sortbin(
     // We want file I/O to occur on 4096-byte boundaries.
     // To ensure this, we want to do I/O on multiples of 4096 records.
     // To ensure this is possible, we need room for ~ 32k records per branch.
-    if (ctx.branch_factor > ctx.memory_size / ctx.record_size / 32768) {
+    if (ctx.memory_size / ctx.record_size / ctx.branch_factor <
+        8 * TRANSFER_ALIGNMENT) {
         throw std::logic_error(
             "Not enough memory for this combination of record size"
             " and branch factor");
@@ -1603,7 +1794,7 @@ int main(int argc, char **argv)
 
     SortContext ctx;
     ctx.record_size = record_size;
-    ctx.memory_size = uint64_t(memory_size) * 1024 * 1024;
+    ctx.memory_size = size_t(memory_size) * 1024 * 1024;
     ctx.branch_factor = branch_factor;
     ctx.flag_unique = flag_unique;
     ctx.flag_verbose = flag_verbose;