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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_H
#define UTIL_STREAM_SORT_H
#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_;
}
ErsatzPRead(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) {
ErsatzPRead(in_, l->Get(), block_size, offset);
l->SetValidSize(block_size);
}
ErsatzPRead(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() {}
};
/** Sort */
template <class Compare, class Combine = NeverCombine> class Sort {
public:
/** Constructs an object capable of sorting */
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_H
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