Commit 942204a4 authored by Philip Pronin's avatar Philip Pronin Committed by Sara Golemon

streaming support for EF compression

Test Plan: fbconfig -r folly/experimental/test:eliasfano_test && fbmake opt -j32

Reviewed By: lucian@fb.com

Subscribers: chaoyc, search-fbcode-diffs@, unicorn-diffs@

FB internal diff: D1474625

Tasks: 4828866
parent af59f4c1
...@@ -32,7 +32,6 @@ ...@@ -32,7 +32,6 @@
#error EliasFanoCoding.h requires x86_64 #error EliasFanoCoding.h requires x86_64
#endif #endif
#include <algorithm>
#include <cstdlib> #include <cstdlib>
#include <limits> #include <limits>
#include <type_traits> #include <type_traits>
...@@ -51,8 +50,7 @@ ...@@ -51,8 +50,7 @@
namespace folly { namespace compression { namespace folly { namespace compression {
struct EliasFanoCompressedList { struct EliasFanoCompressedList {
EliasFanoCompressedList() EliasFanoCompressedList() { }
: size(0), numLowerBits(0) { }
void free() { void free() {
::free(const_cast<unsigned char*>(lower.data())); ::free(const_cast<unsigned char*>(lower.data()));
...@@ -61,8 +59,8 @@ struct EliasFanoCompressedList { ...@@ -61,8 +59,8 @@ struct EliasFanoCompressedList {
::free(const_cast<unsigned char*>(forwardPointers.data())); ::free(const_cast<unsigned char*>(forwardPointers.data()));
} }
size_t size; size_t size = 0;
uint8_t numLowerBits; uint8_t numLowerBits = 0;
// WARNING: EliasFanoCompressedList has no ownership of // WARNING: EliasFanoCompressedList has no ownership of
// lower, upper, skipPointers and forwardPointers. // lower, upper, skipPointers and forwardPointers.
...@@ -106,30 +104,29 @@ struct EliasFanoEncoder { ...@@ -106,30 +104,29 @@ struct EliasFanoEncoder {
return folly::findLastSet(upperBound / size) - 1; return folly::findLastSet(upperBound / size) - 1;
} }
// Requires: input range (begin, end) is sorted (encoding
// crashes if it's not).
// WARNING: encode() mallocates lower, upper, skipPointers // WARNING: encode() mallocates lower, upper, skipPointers
// and forwardPointers. As EliasFanoCompressedList has // and forwardPointers. As EliasFanoCompressedList has
// no ownership of them, you need to call free() explicitly. // no ownership of them, you need to call free() explicitly.
static void encode(const ValueType* list, size_t size,
EliasFanoCompressedList& result) {
encode(list, list + size, result);
}
// Range (begin, end) should be sorted.
template <class RandomAccessIterator> template <class RandomAccessIterator>
static void encode(RandomAccessIterator begin, static EliasFanoCompressedList encode(RandomAccessIterator begin,
RandomAccessIterator end, RandomAccessIterator end) {
EliasFanoCompressedList& result) { if (begin == end) {
CHECK(std::is_sorted(begin, end)); return EliasFanoCompressedList();
}
auto list = begin; EliasFanoEncoder encoder(end - begin, *(end - 1));
const size_t size = end - begin; for (; begin != end; ++begin) {
encoder.add(*begin);
}
return encoder.finish();
}
EliasFanoEncoder(size_t size, ValueType upperBound) {
if (size == 0) { if (size == 0) {
result = EliasFanoCompressedList();
return; return;
} }
const ValueType upperBound = list[size - 1];
uint8_t numLowerBits = defaultNumLowerBits(upperBound, size); uint8_t numLowerBits = defaultNumLowerBits(upperBound, size);
// This is detail::writeBits56 limitation. // This is detail::writeBits56 limitation.
...@@ -144,14 +141,8 @@ struct EliasFanoEncoder { ...@@ -144,14 +141,8 @@ struct EliasFanoEncoder {
// *** Lower bits. // *** Lower bits.
const size_t lowerSize = (numLowerBits * size + 7) / 8; const size_t lowerSize = (numLowerBits * size + 7) / 8;
unsigned char* lower = nullptr;
if (lowerSize > 0) { // numLowerBits != 0 if (lowerSize > 0) { // numLowerBits != 0
lower = static_cast<unsigned char*>(calloc(lowerSize + 7, 1)); lower_ = static_cast<unsigned char*>(calloc(lowerSize + 7, 1));
const ValueType lowerMask = (ValueType(1) << numLowerBits) - 1;
for (size_t i = 0; i < size; ++i) {
const ValueType lowerBits = list[i] & lowerMask;
writeBits56(lower, i * numLowerBits, numLowerBits, lowerBits);
}
} }
// *** Upper bits. // *** Upper bits.
...@@ -161,22 +152,13 @@ struct EliasFanoEncoder { ...@@ -161,22 +152,13 @@ struct EliasFanoEncoder {
(upperBound >> numLowerBits) + // Number of 0-bits to be stored. (upperBound >> numLowerBits) + // Number of 0-bits to be stored.
size; // 1-bits. size; // 1-bits.
const size_t upperSize = (upperSizeBits + 7) / 8; const size_t upperSize = (upperSizeBits + 7) / 8;
unsigned char* const upper = upper_ = static_cast<unsigned char*>(calloc(upperSize + 7, 1));
static_cast<unsigned char*>(calloc(upperSize + 7, 1));
for (size_t i = 0; i < size; ++i) {
const ValueType upperBits = list[i] >> numLowerBits;
const size_t pos = upperBits + i; // upperBits 0-bits and (i + 1) 1-bits.
upper[pos / 8] |= 1U << (pos % 8);
}
// *** Skip pointers. // *** Skip pointers.
// Store (1-indexed) position of every skipQuantum-th // Store (1-indexed) position of every skipQuantum-th
// 0-bit in upper bits sequence. // 0-bit in upper bits sequence.
SkipValueType* skipPointers = nullptr;
size_t numSkipPointers = 0; size_t numSkipPointers = 0;
/* static */ if (skipQuantum != 0) { /* static */ if (skipQuantum != 0) {
// Workaround to avoid 'division by zero' compile-time error.
constexpr size_t q = skipQuantum ?: 1;
/* static */ if (kVersion > 0) { /* static */ if (kVersion > 0) {
CHECK_LT(size, std::numeric_limits<SkipValueType>::max()); CHECK_LT(size, std::numeric_limits<SkipValueType>::max());
} else { } else {
...@@ -186,33 +168,18 @@ struct EliasFanoEncoder { ...@@ -186,33 +168,18 @@ struct EliasFanoEncoder {
// more serialization-friendly way (upperSizeBits isn't known outside of // more serialization-friendly way (upperSizeBits isn't known outside of
// this function, unlike upperSize; thus numSkipPointers could easily be // this function, unlike upperSize; thus numSkipPointers could easily be
// deduced from upperSize). // deduced from upperSize).
numSkipPointers = (8 * upperSize - size) / q; numSkipPointers = (8 * upperSize - size) / (skipQuantum ?: 1);
skipPointers = static_cast<SkipValueType*>( skipPointers_ = static_cast<SkipValueType*>(
numSkipPointers == 0 numSkipPointers == 0
? nullptr ? nullptr
: calloc(numSkipPointers, sizeof(SkipValueType))); : calloc(numSkipPointers, sizeof(SkipValueType)));
for (size_t i = 0, pos = 0; i < size; ++i) {
const ValueType upperBits = list[i] >> numLowerBits;
for (; (pos + 1) * q <= upperBits; ++pos) {
/* static */ if (kVersion > 0) {
// Since version 1, just the number of preceding 1-bits is stored.
skipPointers[pos] = i;
} else {
skipPointers[pos] = i + (pos + 1) * q;
}
}
}
} }
// *** Forward pointers. // *** Forward pointers.
// Store (1-indexed) position of every forwardQuantum-th // Store (1-indexed) position of every forwardQuantum-th
// 1-bit in upper bits sequence. // 1-bit in upper bits sequence.
SkipValueType* forwardPointers = nullptr;
size_t numForwardPointers = 0; size_t numForwardPointers = 0;
/* static */ if (forwardQuantum != 0) { /* static */ if (forwardQuantum != 0) {
// Workaround to avoid 'division by zero' compile-time error.
constexpr size_t q = forwardQuantum ?: 1;
/* static */ if (kVersion > 0) { /* static */ if (kVersion > 0) {
CHECK_LT(upperBound >> numLowerBits, CHECK_LT(upperBound >> numLowerBits,
std::numeric_limits<SkipValueType>::max()); std::numeric_limits<SkipValueType>::max());
...@@ -220,34 +187,74 @@ struct EliasFanoEncoder { ...@@ -220,34 +187,74 @@ struct EliasFanoEncoder {
CHECK_LT(upperSizeBits, std::numeric_limits<SkipValueType>::max()); CHECK_LT(upperSizeBits, std::numeric_limits<SkipValueType>::max());
} }
numForwardPointers = size / q; // '?: 1' is a workaround for false 'division by zero' compile-time error.
forwardPointers = static_cast<SkipValueType*>( numForwardPointers = size / (forwardQuantum ?: 1);
forwardPointers_ = static_cast<SkipValueType*>(
numForwardPointers == 0 numForwardPointers == 0
? nullptr ? nullptr
: malloc(numForwardPointers * sizeof(SkipValueType))); : malloc(numForwardPointers * sizeof(SkipValueType)));
}
// *** Result.
result_.size = size;
result_.numLowerBits = numLowerBits;
result_.lower.reset(lower_, lowerSize);
result_.upper.reset(upper_, upperSize);
result_.skipPointers.reset(
reinterpret_cast<unsigned char*>(skipPointers_),
numSkipPointers * sizeof(SkipValueType));
result_.forwardPointers.reset(
reinterpret_cast<unsigned char*>(forwardPointers_),
numForwardPointers * sizeof(SkipValueType));
}
void add(ValueType value) {
CHECK_GE(value, lastValue_);
for (size_t i = q - 1, pos = 0; i < size; i += q, ++pos) { const auto numLowerBits = result_.numLowerBits;
const ValueType upperBits = list[i] >> numLowerBits; const ValueType upperBits = value >> numLowerBits;
// Upper sequence consists of upperBits 0-bits and (size_ + 1) 1-bits.
const size_t pos = upperBits + size_;
upper_[pos / 8] |= 1U << (pos % 8);
// Append numLowerBits bits to lower sequence.
if (numLowerBits != 0) {
const ValueType lowerBits = value & ((ValueType(1) << numLowerBits) - 1);
writeBits56(lower_, size_ * numLowerBits, numLowerBits, lowerBits);
}
/* static */ if (skipQuantum != 0) {
while ((skipPointersSize_ + 1) * skipQuantum <= upperBits) {
/* static */ if (kVersion > 0) {
// Since version 1, just the number of preceding 1-bits is stored.
skipPointers_[skipPointersSize_] = size_;
} else {
skipPointers_[skipPointersSize_] =
size_ + (skipPointersSize_ + 1) * skipQuantum;
}
++skipPointersSize_;
}
}
/* static */ if (forwardQuantum != 0) {
if ((size_ + 1) % forwardQuantum == 0) {
const auto pos = size_ / forwardQuantum;
/* static */ if (kVersion > 0) { /* static */ if (kVersion > 0) {
// Since version 1, just the number of preceding 0-bits is stored. // Since version 1, just the number of preceding 0-bits is stored.
forwardPointers[pos] = upperBits; forwardPointers_[pos] = upperBits;
} else { } else {
forwardPointers[pos] = upperBits + i + 1; forwardPointers_[pos] = upperBits + size_ + 1;
} }
} }
} }
// *** Result. lastValue_ = value;
result.size = size; ++size_;
result.numLowerBits = numLowerBits; }
result.lower.reset(lower, lowerSize);
result.upper.reset(upper, upperSize); const EliasFanoCompressedList& finish() const {
result.skipPointers.reset( CHECK_EQ(size_, result_.size);
reinterpret_cast<unsigned char*>(skipPointers), return result_;
numSkipPointers * sizeof(SkipValueType));
result.forwardPointers.reset(
reinterpret_cast<unsigned char*>(forwardPointers),
numForwardPointers * sizeof(SkipValueType));
} }
private: private:
...@@ -261,6 +268,17 @@ struct EliasFanoEncoder { ...@@ -261,6 +268,17 @@ struct EliasFanoEncoder {
ptrv |= value << (pos % 8); ptrv |= value << (pos % 8);
folly::storeUnaligned<uint64_t>(ptr, ptrv); folly::storeUnaligned<uint64_t>(ptr, ptrv);
} }
unsigned char* lower_ = nullptr;
unsigned char* upper_ = nullptr;
SkipValueType* skipPointers_ = nullptr;
SkipValueType* forwardPointers_ = nullptr;
ValueType lastValue_ = 0;
size_t size_ = 0;
size_t skipPointersSize_ = 0;
EliasFanoCompressedList result_;
}; };
// NOTE: It's recommended to compile EF coding with -msse4.2, starting // NOTE: It's recommended to compile EF coding with -msse4.2, starting
......
...@@ -177,9 +177,8 @@ void testGoTo(const std::vector<uint32_t>& data, const List& list) { ...@@ -177,9 +177,8 @@ void testGoTo(const std::vector<uint32_t>& data, const List& list) {
template <class Reader, class Encoder> template <class Reader, class Encoder>
void testEmpty() { void testEmpty() {
typename Encoder::CompressedList list;
const typename Encoder::ValueType* const data = nullptr; const typename Encoder::ValueType* const data = nullptr;
Encoder::encode(data, 0, list); auto list = Encoder::encode(data, data);
{ {
Reader reader(list); Reader reader(list);
EXPECT_FALSE(reader.next()); EXPECT_FALSE(reader.next());
...@@ -198,8 +197,7 @@ void testEmpty() { ...@@ -198,8 +197,7 @@ void testEmpty() {
template <class Reader, class Encoder> template <class Reader, class Encoder>
void testAll(const std::vector<uint32_t>& data) { void testAll(const std::vector<uint32_t>& data) {
typename Encoder::CompressedList list; auto list = Encoder::encode(data.begin(), data.end());
Encoder::encode(data.begin(), data.end(), list);
testNext<Reader>(data, list); testNext<Reader>(data, list);
testSkip<Reader>(data, list); testSkip<Reader>(data, list);
testSkipTo<Reader>(data, list); testSkipTo<Reader>(data, list);
......
...@@ -82,6 +82,9 @@ typedef EliasFanoReader<Encoder> Reader; ...@@ -82,6 +82,9 @@ typedef EliasFanoReader<Encoder> Reader;
std::vector<uint32_t> data; std::vector<uint32_t> data;
std::vector<size_t> order; std::vector<size_t> order;
std::vector<uint32_t> encodeSmallData;
std::vector<uint32_t> encodeLargeData;
typename Encoder::CompressedList list; typename Encoder::CompressedList list;
void init() { void init() {
...@@ -89,7 +92,7 @@ void init() { ...@@ -89,7 +92,7 @@ void init() {
data = generateRandomList(100 * 1000, 10 * 1000 * 1000, gen); data = generateRandomList(100 * 1000, 10 * 1000 * 1000, gen);
//data = loadList("/home/philipp/pl_test_dump.txt"); //data = loadList("/home/philipp/pl_test_dump.txt");
Encoder::encode(data.data(), data.size(), bm::list); list = Encoder::encode(data.begin(), data.end());
order.clear(); order.clear();
order.reserve(data.size()); order.reserve(data.size());
...@@ -97,6 +100,9 @@ void init() { ...@@ -97,6 +100,9 @@ void init() {
order.push_back(i); order.push_back(i);
} }
std::shuffle(order.begin(), order.end(), gen); std::shuffle(order.begin(), order.end(), gen);
encodeSmallData = generateRandomList(10, 100 * 1000, gen);
encodeLargeData = generateRandomList(1000 * 1000, 100 * 1000 * 1000, gen);
} }
void free() { void free() {
...@@ -133,6 +139,8 @@ BENCHMARK(SkipTo1_SkipQ128_1M) { ...@@ -133,6 +139,8 @@ BENCHMARK(SkipTo1_SkipQ128_1M) {
bmSkipTo<bm::Reader>(bm::list, bm::data, 1, bm::k1M); bmSkipTo<bm::Reader>(bm::list, bm::data, 1, bm::k1M);
} }
BENCHMARK_DRAW_LINE();
BENCHMARK(SkipTo10_SkipQ128_1M) { BENCHMARK(SkipTo10_SkipQ128_1M) {
bmSkipTo<bm::Reader>(bm::list, bm::data, 10, bm::k1M); bmSkipTo<bm::Reader>(bm::list, bm::data, 10, bm::k1M);
} }
...@@ -145,8 +153,22 @@ BENCHMARK(SkipTo1000_SkipQ128_1M) { ...@@ -145,8 +153,22 @@ BENCHMARK(SkipTo1000_SkipQ128_1M) {
bmSkipTo<bm::Reader>(bm::list, bm::data, 1000, bm::k1M); bmSkipTo<bm::Reader>(bm::list, bm::data, 1000, bm::k1M);
} }
BENCHMARK_DRAW_LINE();
BENCHMARK(Encode_10) {
auto list = bm::Encoder::encode(bm::encodeSmallData.begin(),
bm::encodeSmallData.end());
list.free();
}
BENCHMARK(Encode_1M) {
auto list = bm::Encoder::encode(bm::encodeLargeData.begin(),
bm::encodeLargeData.end());
list.free();
}
#if 0 #if 0
Intel Xeon CPU E5-2660 @ 2.7GHz (turbo on), using instructions::Fast. Intel(R) Xeon(R) CPU E5-2660 @ 2.7GHz (turbo on), using instructions::Fast.
============================================================================ ============================================================================
folly/experimental/test/EliasFanoCodingTest.cpp relative time/iter iters/s folly/experimental/test/EliasFanoCodingTest.cpp relative time/iter iters/s
...@@ -157,10 +179,14 @@ Skip10_ForwarQ128_1M 13.69ms 73.03 ...@@ -157,10 +179,14 @@ Skip10_ForwarQ128_1M 13.69ms 73.03
Skip100_ForwardQ128_1M 26.76ms 37.37 Skip100_ForwardQ128_1M 26.76ms 37.37
Skip1000_ForwardQ128_1M 20.66ms 48.40 Skip1000_ForwardQ128_1M 20.66ms 48.40
GoTo_ForwardQ128_1M 43.75ms 22.86 GoTo_ForwardQ128_1M 43.75ms 22.86
----------------------------------------------------------------------------
SkipTo1_SkipQ128_1M 9.74ms 102.70 SkipTo1_SkipQ128_1M 9.74ms 102.70
SkipTo10_SkipQ128_1M 30.62ms 32.66 SkipTo10_SkipQ128_1M 30.62ms 32.66
SkipTo100_SkipQ128_1M 37.70ms 26.53 SkipTo100_SkipQ128_1M 37.70ms 26.53
SkipTo1000_SkipQ128_1M 31.14ms 32.11 SkipTo1000_SkipQ128_1M 31.14ms 32.11
----------------------------------------------------------------------------
Encode_10 208.16ns 4.80M
Encode_1M 8.90ms 112.37
============================================================================ ============================================================================
#endif #endif
......
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