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Merge pull request #10531 from CurtizJ/polymorphic-parts-2

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Fix index corruption in merges with compact parts.
This commit is contained in:
alesapin 2020-04-30 12:15:25 +03:00 committed by GitHub
commit 15e8f37839
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8 changed files with 234 additions and 72 deletions
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71
src/Storages/MergeTree/IMergeTreeDataPartWriter.cpp
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@ -71,8 +71,7 @@ IMergeTreeDataPartWriter::IMergeTreeDataPartWriter(
const String & marks_file_extension_,
const CompressionCodecPtr & default_codec_,
const MergeTreeWriterSettings & settings_,
const MergeTreeIndexGranularity & index_granularity_,
bool need_finish_last_granule_)
const MergeTreeIndexGranularity & index_granularity_)
: disk(std::move(disk_))
, part_path(part_path_)
, storage(storage_)
@ -84,7 +83,6 @@ IMergeTreeDataPartWriter::IMergeTreeDataPartWriter(
, settings(settings_)
, compute_granularity(index_granularity.empty())
, with_final_mark(storage.getSettings()->write_final_mark && settings.can_use_adaptive_granularity)
, need_finish_last_granule(need_finish_last_granule_)
{
if (settings.blocks_are_granules_size && !index_granularity.empty())
throw Exception("Can't take information about index granularity from blocks, when non empty index_granularity array specified", ErrorCodes::LOGICAL_ERROR);
@ -95,15 +93,15 @@ IMergeTreeDataPartWriter::IMergeTreeDataPartWriter(
IMergeTreeDataPartWriter::~IMergeTreeDataPartWriter() = default;
static void fillIndexGranularityImpl(
/// Implemetation is splitted into static functions for ability
/// of making unit tests without creation instance of IMergeTreeDataPartWriter,
/// which requires a lot of dependencies and access to filesystem.
static size_t computeIndexGranularityImpl(
const Block & block,
size_t index_granularity_bytes,
size_t fixed_index_granularity_rows,
bool blocks_are_granules,
size_t index_offset,
MergeTreeIndexGranularity & index_granularity,
bool can_use_adaptive_index_granularity,
bool need_finish_last_granule = false)
bool can_use_adaptive_index_granularity)
{
size_t rows_in_block = block.rows();
size_t index_granularity_for_block;
@ -130,43 +128,37 @@ static void fillIndexGranularityImpl(
/// We should be less or equal than fixed index granularity
index_granularity_for_block = std::min(fixed_index_granularity_rows, index_granularity_for_block);
size_t current_row;
for (current_row = index_offset; current_row < rows_in_block; current_row += index_granularity_for_block)
{
size_t rows_left_in_block = rows_in_block - current_row;
/// Try to extend last granule if it's needed and block is large enough
/// or it shouldn't be first in granule (index_offset != 0).
if (need_finish_last_granule && rows_left_in_block < index_granularity_for_block
&& (rows_in_block >= index_granularity_for_block || index_offset != 0))
{
// If enough rows are left, create a new granule. Otherwise, extend previous granule.
// So, real size of granule differs from index_granularity_for_block not more than 50%.
if (rows_left_in_block * 2 >= index_granularity_for_block)
index_granularity.appendMark(rows_left_in_block);
else
index_granularity.addRowsToLastMark(rows_left_in_block);
return index_granularity_for_block;
}
else
static void fillIndexGranularityImpl(
MergeTreeIndexGranularity & index_granularity,
size_t index_offset,
size_t index_granularity_for_block,
size_t rows_in_block)
{
for (size_t current_row = index_offset; current_row < rows_in_block; current_row += index_granularity_for_block)
index_granularity.appendMark(index_granularity_for_block);
}
}
}
void IMergeTreeDataPartWriter::fillIndexGranularity(const Block & block)
size_t IMergeTreeDataPartWriter::computeIndexGranularity(const Block & block)
{
const auto storage_settings = storage.getSettings();
fillIndexGranularityImpl(
return computeIndexGranularityImpl(
block,
storage_settings->index_granularity_bytes,
storage_settings->index_granularity,
settings.blocks_are_granules_size,
index_offset,
settings.can_use_adaptive_granularity);
}
void IMergeTreeDataPartWriter::fillIndexGranularity(size_t index_granularity_for_block, size_t rows_in_block)
{
fillIndexGranularityImpl(
index_granularity,
settings.can_use_adaptive_granularity,
need_finish_last_granule);
index_offset,
index_granularity_for_block,
rows_in_block);
}
void IMergeTreeDataPartWriter::initPrimaryIndex()
@ -225,21 +217,22 @@ void IMergeTreeDataPartWriter::calculateAndSerializePrimaryIndex(const Block & p
/// Write index. The index contains Primary Key value for each `index_granularity` row.
for (size_t i = index_offset; i < rows;)
size_t current_row = index_offset;
size_t total_marks = index_granularity.getMarksCount();
while (index_mark < total_marks && current_row < rows)
{
if (storage.hasPrimaryKey())
{
for (size_t j = 0; j < primary_columns_num; ++j)
{
const auto & primary_column = primary_index_block.getByPosition(j);
index_columns[j]->insertFrom(*primary_column.column, i);
primary_column.type->serializeBinary(*primary_column.column, i, *index_stream);
index_columns[j]->insertFrom(*primary_column.column, current_row);
primary_column.type->serializeBinary(*primary_column.column, current_row, *index_stream);
}
}
i += index_granularity.getMarkRows(current_mark++);
if (current_mark >= index_granularity.getMarksCount())
break;
current_row += index_granularity.getMarkRows(index_mark++);
}
/// store last index row to write final mark at the end of column

27
src/Storages/MergeTree/IMergeTreeDataPartWriter.h
View File

@ -69,8 +69,7 @@ public:
const String & marks_file_extension,
const CompressionCodecPtr & default_codec,
const MergeTreeWriterSettings & settings,
const MergeTreeIndexGranularity & index_granularity,
bool need_finish_last_granule);
const MergeTreeIndexGranularity & index_granularity);
virtual ~IMergeTreeDataPartWriter();
@ -87,9 +86,6 @@ public:
/// calling calculations of primary and skip indices.
void next();
/// Count index_granularity for block and store in `index_granularity`
void fillIndexGranularity(const Block & block);
const MergeTreeIndexGranularity & getIndexGranularity() const { return index_granularity; }
Columns releaseIndexColumns()
@ -112,6 +108,13 @@ public:
void finishSkipIndicesSerialization(MergeTreeData::DataPart::Checksums & checksums);
protected:
/// Count index_granularity for block and store in `index_granularity`
size_t computeIndexGranularity(const Block & block);
virtual void fillIndexGranularity(size_t index_granularity_for_block, size_t rows_in_block);
size_t getCurrentMark() const { return current_mark; }
size_t getIndexOffset() const { return index_offset; }
using SerializationState = IDataType::SerializeBinaryBulkStatePtr;
using SerializationStates = std::unordered_map<String, SerializationState>;
@ -131,12 +134,6 @@ protected:
bool compute_granularity;
bool with_final_mark;
bool need_finish_last_granule;
size_t current_mark = 0;
/// The offset to the first row of the block for which you want to write the index.
size_t index_offset = 0;
size_t next_mark = 0;
size_t next_index_offset = 0;
@ -163,6 +160,14 @@ protected:
/// To correctly write Nested elements column-by-column.
WrittenOffsetColumns * written_offset_columns = nullptr;
private:
/// Data is already written up to this mark.
size_t current_mark = 0;
/// The offset to the first row of the block for which you want to write the index.
size_t index_offset = 0;
/// Index is already serialized up to this mark.
size_t index_mark = 0;
};
}

47
src/Storages/MergeTree/MergeTreeDataPartWriterCompact.cpp
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@ -18,7 +18,7 @@ MergeTreeDataPartWriterCompact::MergeTreeDataPartWriterCompact(
: IMergeTreeDataPartWriter(disk_, part_path_,
storage_, columns_list_,
indices_to_recalc_, marks_file_extension_,
default_codec_, settings_, index_granularity_, true)
default_codec_, settings_, index_granularity_)
{
using DataPart = MergeTreeDataPartCompact;
String data_file_name = DataPart::DATA_FILE_NAME;
@ -42,7 +42,10 @@ void MergeTreeDataPartWriterCompact::write(
/// if it's unknown (in case of insert data or horizontal merge,
/// but not in case of vertical merge)
if (compute_granularity)
fillIndexGranularity(block);
{
size_t index_granularity_for_block = computeIndexGranularity(block);
fillIndexGranularity(index_granularity_for_block, block.rows());
}
Block result_block;
@ -88,7 +91,7 @@ void MergeTreeDataPartWriterCompact::write(
void MergeTreeDataPartWriterCompact::writeBlock(const Block & block)
{
size_t total_rows = block.rows();
size_t from_mark = current_mark;
size_t from_mark = getCurrentMark();
size_t current_row = 0;
while (current_row < total_rows)
@ -163,6 +166,44 @@ void MergeTreeDataPartWriterCompact::finishDataSerialization(IMergeTreeDataPart:
stream.reset();
}
static void fillIndexGranularityImpl(
MergeTreeIndexGranularity & index_granularity,
size_t index_offset,
size_t index_granularity_for_block,
size_t rows_in_block)
{
for (size_t current_row = index_offset; current_row < rows_in_block; current_row += index_granularity_for_block)
{
size_t rows_left_in_block = rows_in_block - current_row;
/// Try to extend last granule if block is large enough
/// or it isn't first in granule (index_offset != 0).
if (rows_left_in_block < index_granularity_for_block &&
(rows_in_block >= index_granularity_for_block || index_offset != 0))
{
// If enough rows are left, create a new granule. Otherwise, extend previous granule.
// So, real size of granule differs from index_granularity_for_block not more than 50%.
if (rows_left_in_block * 2 >= index_granularity_for_block)
index_granularity.appendMark(rows_left_in_block);
else
index_granularity.addRowsToLastMark(rows_left_in_block);
}
else
{
index_granularity.appendMark(index_granularity_for_block);
}
}
}
void MergeTreeDataPartWriterCompact::fillIndexGranularity(size_t index_granularity_for_block, size_t rows_in_block)
{
fillIndexGranularityImpl(
index_granularity,
getIndexOffset(),
index_granularity_for_block,
rows_in_block);
}
void MergeTreeDataPartWriterCompact::ColumnsBuffer::add(MutableColumns && columns)
{
if (accumulated_columns.empty())

3
src/Storages/MergeTree/MergeTreeDataPartWriterCompact.h
View File

@ -23,6 +23,9 @@ public:
void finishDataSerialization(IMergeTreeDataPart::Checksums & checksums) override;
protected:
void fillIndexGranularity(size_t index_granularity_for_block, size_t rows_in_block) override;
private:
/// Write single granule of one column (rows between 2 marks)
void writeColumnSingleGranule(

14
src/Storages/MergeTree/MergeTreeDataPartWriterWide.cpp
View File

@ -24,7 +24,7 @@ MergeTreeDataPartWriterWide::MergeTreeDataPartWriterWide(
const MergeTreeIndexGranularity & index_granularity_)
: IMergeTreeDataPartWriter(disk_, part_path_,
storage_, columns_list_, indices_to_recalc_,
marks_file_extension_, default_codec_, settings_, index_granularity_, false)
marks_file_extension_, default_codec_, settings_, index_granularity_)
{
const auto & columns = storage.getColumns();
for (const auto & it : columns_list)
@ -85,7 +85,10 @@ void MergeTreeDataPartWriterWide::write(const Block & block,
/// if it's unknown (in case of insert data or horizontal merge,
/// but not in case of vertical merge)
if (compute_granularity)
fillIndexGranularity(block);
{
size_t index_granularity_for_block = computeIndexGranularity(block);
fillIndexGranularity(index_granularity_for_block, block.rows());
}
auto offset_columns = written_offset_columns ? *written_offset_columns : WrittenOffsetColumns{};
@ -206,17 +209,18 @@ void MergeTreeDataPartWriterWide::writeColumn(
size_t total_rows = column.size();
size_t current_row = 0;
size_t current_column_mark = current_mark;
size_t current_column_mark = getCurrentMark();
size_t current_index_offset = getIndexOffset();
while (current_row < total_rows)
{
size_t rows_to_write;
bool write_marks = true;
/// If there is `index_offset`, then the first mark goes not immediately, but after this number of rows.
if (current_row == 0 && index_offset != 0)
if (current_row == 0 && current_index_offset != 0)
{
write_marks = false;
rows_to_write = index_offset;
rows_to_write = current_index_offset;
}
else
{

28
src/Storages/tests/gtest_aux_funcs_for_adaptive_granularity.cpp
View File

@ -25,14 +25,16 @@ TEST(AdaptiveIndexGranularity, FillGranularityToyTests)
EXPECT_EQ(block1.bytes(), 80);
{ /// Granularity bytes are not set. Take default index_granularity.
MergeTreeIndexGranularity index_granularity;
fillIndexGranularityImpl(block1, 0, 100, false, 0, index_granularity, false);
auto granularity = computeIndexGranularityImpl(block1, 0, 100, false, false);
fillIndexGranularityImpl(index_granularity, 0, granularity, block1.rows());
EXPECT_EQ(index_granularity.getMarksCount(), 1);
EXPECT_EQ(index_granularity.getMarkRows(0), 100);
}
{ /// Granule size is less than block size. Block contains multiple granules.
MergeTreeIndexGranularity index_granularity;
fillIndexGranularityImpl(block1, 16, 100, false, 0, index_granularity, true);
auto granularity = computeIndexGranularityImpl(block1, 16, 100, false, true);
fillIndexGranularityImpl(index_granularity, 0, granularity, block1.rows());
EXPECT_EQ(index_granularity.getMarksCount(), 5); /// First granule with 8 rows, and second with 1 row
for (size_t i = 0; i < index_granularity.getMarksCount(); ++i)
EXPECT_EQ(index_granularity.getMarkRows(i), 2);
@ -41,7 +43,8 @@ TEST(AdaptiveIndexGranularity, FillGranularityToyTests)
{ /// Granule size is more than block size. Whole block (and maybe more) can be placed in single granule.
MergeTreeIndexGranularity index_granularity;
fillIndexGranularityImpl(block1, 512, 100, false, 0, index_granularity, true);
auto granularity = computeIndexGranularityImpl(block1, 512, 100, false, true);
fillIndexGranularityImpl(index_granularity, 0, granularity, block1.rows());
EXPECT_EQ(index_granularity.getMarksCount(), 1);
for (size_t i = 0; i < index_granularity.getMarksCount(); ++i)
EXPECT_EQ(index_granularity.getMarkRows(i), 64);
@ -50,7 +53,8 @@ TEST(AdaptiveIndexGranularity, FillGranularityToyTests)
{ /// Blocks with granule size
MergeTreeIndexGranularity index_granularity;
fillIndexGranularityImpl(block1, 1, 100, true, 0, index_granularity, true);
auto granularity = computeIndexGranularityImpl(block1, 1, 100, true, true);
fillIndexGranularityImpl(index_granularity, 0, granularity, block1.rows());
EXPECT_EQ(index_granularity.getMarksCount(), 1);
for (size_t i = 0; i < index_granularity.getMarksCount(); ++i)
EXPECT_EQ(index_granularity.getMarkRows(i), block1.rows());
@ -58,7 +62,8 @@ TEST(AdaptiveIndexGranularity, FillGranularityToyTests)
{ /// Shift in index offset
MergeTreeIndexGranularity index_granularity;
fillIndexGranularityImpl(block1, 16, 100, false, 6, index_granularity, true);
auto granularity = computeIndexGranularityImpl(block1, 16, 100, false, true);
fillIndexGranularityImpl(index_granularity, 6, granularity, block1.rows());
EXPECT_EQ(index_granularity.getMarksCount(), 2);
for (size_t i = 0; i < index_granularity.getMarksCount(); ++i)
EXPECT_EQ(index_granularity.getMarkRows(i), 2);
@ -74,7 +79,10 @@ TEST(AdaptiveIndexGranularity, FillGranularitySequenceOfBlocks)
auto block3 = getBlockWithSize(65536, 8);
MergeTreeIndexGranularity index_granularity;
for (const auto & block : {block1, block2, block3})
fillIndexGranularityImpl(block, 1024, 8192, false, 0, index_granularity, true);
{
auto granularity = computeIndexGranularityImpl(block, 1024, 8192, false, true);
fillIndexGranularityImpl(index_granularity, 0, granularity, block.rows());
}
EXPECT_EQ(index_granularity.getMarksCount(), 192); /// granules
for (size_t i = 0; i < index_granularity.getMarksCount(); ++i)
@ -87,7 +95,10 @@ TEST(AdaptiveIndexGranularity, FillGranularitySequenceOfBlocks)
EXPECT_EQ(block1.rows() + block2.rows() + block3.rows(), 3136);
MergeTreeIndexGranularity index_granularity;
for (const auto & block : {block1, block2, block3})
fillIndexGranularityImpl(block, 1024, 8192, false, 0, index_granularity, true);
{
auto granularity = computeIndexGranularityImpl(block, 1024, 8192, false, true);
fillIndexGranularityImpl(index_granularity, 0, granularity, block.rows());
}
EXPECT_EQ(index_granularity.getMarksCount(), 98); /// granules
for (size_t i = 0; i < index_granularity.getMarksCount(); ++i)
@ -105,7 +116,8 @@ TEST(AdaptiveIndexGranularity, FillGranularitySequenceOfBlocks)
size_t index_offset = 0;
for (const auto & block : {block1, block2, block3})
{
fillIndexGranularityImpl(block, 16384, 8192, false, index_offset, index_granularity, true);
auto granularity = computeIndexGranularityImpl(block, 16384, 8192, false, true);
fillIndexGranularityImpl(index_granularity, index_offset, granularity, block.rows());
index_offset = index_granularity.getLastMarkRows() - block.rows();
}
EXPECT_EQ(index_granularity.getMarksCount(), 1); /// granules

81
src/Storages/tests/gtest_aux_funcs_for_adaptive_granularity_compact_parts.cpp Normal file
View File

@ -0,0 +1,81 @@
#include <gtest/gtest.h>
#include <Core/Block.h>
#include <Columns/ColumnVector.h>
// I know that inclusion of .cpp is not good at all
#include <Storages/MergeTree/MergeTreeDataPartWriterCompact.cpp>
using namespace DB;
TEST(IndexGranularityCompactParts, FillGranularitySequenceOfBlocks)
{
{ /// Three blocks in one granule.
size_t rows = 8;
size_t granularity = 32;
MergeTreeIndexGranularity index_granularity;
size_t index_offset = 0;
size_t rows_written = 0;
for (size_t i = 0; i < 3; ++i)
{
fillIndexGranularityImpl(index_granularity, index_offset, granularity, rows);
rows_written += rows;
index_offset = granularity - rows_written;
}
EXPECT_EQ(index_granularity.getMarksCount(), 1); /// granules
/// It's ok, that granularity is higher than actual number of row.
/// It will be corrected in CompactWriter.
EXPECT_EQ(index_granularity.getMarkRows(0), granularity);
}
{ /// Granule is extended with small block
size_t rows1 = 30;
size_t rows2 = 8;
size_t granularity = 32;
MergeTreeIndexGranularity index_granularity;
size_t index_offset = 0;
fillIndexGranularityImpl(index_granularity, index_offset, granularity, rows1);
index_offset = granularity - rows1;
fillIndexGranularityImpl(index_granularity, index_offset, granularity, rows2);
EXPECT_EQ(index_granularity.getMarksCount(), 1);
EXPECT_EQ(index_granularity.getMarkRows(0), rows1 + rows2);
}
{ /// New granule is created with large block;
size_t rows1 = 30;
size_t rows2 = 25;
size_t granularity = 32;
MergeTreeIndexGranularity index_granularity;
size_t index_offset = 0;
fillIndexGranularityImpl(index_granularity, index_offset, granularity, rows1);
index_offset = granularity - rows1;
fillIndexGranularityImpl(index_granularity, index_offset, granularity, rows2);
EXPECT_EQ(index_granularity.getMarksCount(), 2);
EXPECT_EQ(index_granularity.getMarkRows(0), granularity);
EXPECT_EQ(index_granularity.getMarkRows(1), rows1 + rows2 - granularity);
}
{ /// Three large blocks
size_t rows = 40;
size_t granularity = 32;
MergeTreeIndexGranularity index_granularity;
size_t index_offset = 0;
for (size_t i = 0; i < 3; ++i)
fillIndexGranularityImpl(index_granularity, index_offset, granularity, rows);
EXPECT_EQ(index_granularity.getMarksCount(), 3);
for (size_t i = 0; i < 3; ++i)
EXPECT_EQ(index_granularity.getMarkRows(i), rows);
}
}

23
tests/integration/test_polymorphic_parts/test.py
View File

@ -2,6 +2,8 @@ import time
import pytest
import random
import string
import os
import struct
from helpers.test_tools import TSV
from helpers.test_tools import assert_eq_with_retry
@ -260,3 +262,24 @@ def test_polymorphic_parts_non_adaptive(start_cluster):
"WHERE table = 'non_adaptive_table' AND active GROUP BY part_type ORDER BY part_type")) == TSV("Wide\t2\n")
assert node1.contains_in_log("<Warning> default.non_adaptive_table: Table can't create parts with adaptive granularity")
def test_polymorphic_parts_index(start_cluster):
node1.query('''
CREATE TABLE index_compact(a UInt32, s String)
ENGINE = MergeTree ORDER BY a
SETTINGS min_rows_for_wide_part = 1000, index_granularity = 128, merge_max_block_size = 100''')
node1.query("INSERT INTO index_compact SELECT number, toString(number) FROM numbers(100)")
node1.query("INSERT INTO index_compact SELECT number, toString(number) FROM numbers(30)")
node1.query("OPTIMIZE TABLE index_compact FINAL")
assert node1.query("SELECT part_type FROM system.parts WHERE table = 'index_compact' AND active") == "Compact\n"
assert node1.query("SELECT marks FROM system.parts WHERE table = 'index_compact' AND active") == "2\n"
index_path = os.path.join(node1.path, "database/data/default/index_compact/all_1_2_1/primary.idx")
f = open(index_path, 'rb')
assert os.path.getsize(index_path) == 8
assert struct.unpack('I', f.read(4))[0] == 0
assert struct.unpack('I', f.read(4))[0] == 99