Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

fixing issue 1404 #1460

Merged
merged 1 commit into from
Apr 12, 2023
Merged
Show file tree
Hide file tree
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
5 changes: 4 additions & 1 deletion src/common/task_system/task_scheduler.cpp
Original file line number Diff line number Diff line change
Expand Up @@ -69,8 +69,11 @@ void TaskScheduler::scheduleTaskAndWaitOrError(
}
auto scheduledTask = scheduleTask(task);
while (!task->isCompleted()) {
if (context->clientContext->isTimeOutEnabled()) {
if (context != nullptr && context->clientContext->isTimeOutEnabled()) {
interruptTaskIfTimeOutNoLock(context);
} else if (task->hasException()) {
// Interrupt tasks that errored, so other threads can stop working on them early.
context->clientContext->interrupt();
}
std::this_thread::sleep_for(
std::chrono::microseconds(THREAD_SLEEP_TIME_WHEN_WAITING_IN_MICROS));
Expand Down
2 changes: 1 addition & 1 deletion src/include/common/constants.h
Original file line number Diff line number Diff line change
Expand Up @@ -49,7 +49,7 @@ struct BufferPoolConstants {
// `EvictionQueue::removeNonEvictableCandidates()` for more details.
static constexpr uint64_t EVICTION_QUEUE_PURGING_INTERVAL = 1024;
// The default max size for a VMRegion.
static constexpr uint64_t DEFAULT_VM_REGION_MAX_SIZE = (uint64_t)1 << 45; // (32TB)
static constexpr uint64_t DEFAULT_VM_REGION_MAX_SIZE = (uint64_t)1 << 43; // (8TB)

static constexpr uint64_t DEFAULT_BUFFER_POOL_SIZE_FOR_TESTING = 1ull << 26; // (64MB)
};
Expand Down
2 changes: 0 additions & 2 deletions src/include/main/client_context.h
Original file line number Diff line number Diff line change
Expand Up @@ -40,8 +40,6 @@ class ClientContext {

inline bool isTimeOutEnabled() const { return timeoutInMS != 0; }

inline uint64_t getTimeOutMS() const { return timeoutInMS; }

void startTimingIfEnabled();

private:
Expand Down
19 changes: 12 additions & 7 deletions src/include/storage/copier/copy_task.h
Original file line number Diff line number Diff line change
Expand Up @@ -7,14 +7,13 @@ namespace storage {

class CopyTask : public common::Task {
public:
// CopyCSV tasks are intended to be tasks on which only 1 thread works.
CopyTask() : Task(1){};
CopyTask(uint64_t numThreads) : Task(numThreads){};
};

template<typename F>
class ParameterizedCopyTask : public CopyTask {
public:
ParameterizedCopyTask(F&& func) : f(func){};
ParameterizedCopyTask(F&& func, uint64_t numThreads = 1) : CopyTask(numThreads), f(func){};
void run() override { f(); }

private:
Expand All @@ -25,15 +24,21 @@ class CopyTaskFactory {

private:
template<typename F>
static std::shared_ptr<CopyTask> createCopyTaskInternal(F&& f) {
return std::shared_ptr<CopyTask>(new ParameterizedCopyTask<F>(std::forward<F>(f)));
static std::shared_ptr<CopyTask> createCopyTaskInternal(F&& f, uint64_t numThreads = 1) {
return std::shared_ptr<CopyTask>(
new ParameterizedCopyTask<F>(std::forward<F>(f), numThreads));
};

public:
template<typename F, typename... Args>
static std::shared_ptr<CopyTask> createCopyTask(F function, Args&&... args) {
return std::shared_ptr<CopyTask>(
createCopyTaskInternal(std::move(std::bind(function, args...))));
return createParallelCopyTask(1 /* num threads */, function, args...);
};

template<typename F, typename... Args>
static std::shared_ptr<CopyTask> createParallelCopyTask(
uint64_t numThreads, F function, Args&&... args) {
return createCopyTaskInternal(std::move(std::bind(function, args...)), numThreads);
};
};
} // namespace storage
Expand Down
134 changes: 116 additions & 18 deletions src/include/storage/copier/node_copier.h
Original file line number Diff line number Diff line change
Expand Up @@ -8,9 +8,117 @@
namespace kuzu {
namespace storage {

using lock_t = std::unique_lock<std::mutex>;

using set_element_func_t = std::function<void(NodeInMemColumn* column,
InMemColumnChunk* columnChunk, common::offset_t nodeOffset, const std::string& data)>;

template<typename MORSEL_T>
class NodeCopyMorsel {

public:
static constexpr common::block_idx_t INVALID_BLOCK_IDX = -1ull;

public:
NodeCopyMorsel(common::offset_t startOffset, common::block_idx_t blockIdx)
: startOffset{startOffset}, blockIdx{blockIdx} {};

virtual ~NodeCopyMorsel() = default;

virtual const std::vector<std::shared_ptr<MORSEL_T>>& getArrowColumns() = 0;

bool success() { return blockIdx != INVALID_BLOCK_IDX; }

public:
common::offset_t startOffset;
common::block_idx_t blockIdx;
};

class CSVNodeCopyMorsel : public NodeCopyMorsel<arrow::Array> {

public:
CSVNodeCopyMorsel(std::shared_ptr<arrow::RecordBatch> recordBatch, common::offset_t startOffset,
common::block_idx_t blockIdx)
: NodeCopyMorsel{startOffset, blockIdx}, recordBatch{recordBatch} {};

const std::vector<std::shared_ptr<arrow::Array>>& getArrowColumns() override {
return recordBatch->columns();
}

private:
std::shared_ptr<arrow::RecordBatch> recordBatch;
};

class ParquetNodeCopyMorsel : public NodeCopyMorsel<arrow::ChunkedArray> {

public:
ParquetNodeCopyMorsel(std::shared_ptr<arrow::Table> currTable, common::offset_t startOffset,
common::block_idx_t blockIdx)
: NodeCopyMorsel{startOffset, blockIdx}, currTable{currTable} {};

const std::vector<std::shared_ptr<arrow::ChunkedArray>>& getArrowColumns() override {
return currTable->columns();
}

private:
std::shared_ptr<arrow::Table> currTable;
};

template<typename T1, typename T2>
class NodeCopySharedState {

public:
NodeCopySharedState(
std::string filePath, HashIndexBuilder<T1>* pkIndex, common::offset_t startOffset)
: filePath{filePath}, pkIndex{pkIndex}, startOffset{startOffset}, blockIdx{0} {};

virtual ~NodeCopySharedState() = default;

virtual std::unique_ptr<NodeCopyMorsel<T2>> getMorsel() = 0;

public:
std::string filePath;
HashIndexBuilder<T1>* pkIndex;
common::offset_t startOffset;

protected:
common::block_idx_t blockIdx;
std::mutex mtx;
};

template<typename T>
class CSVNodeCopySharedState : public NodeCopySharedState<T, arrow::Array> {

public:
CSVNodeCopySharedState(std::string filePath, HashIndexBuilder<T>* pkIndex,
common::offset_t startOffset,
std::shared_ptr<arrow::csv::StreamingReader> csvStreamingReader)
: NodeCopySharedState<T, arrow::Array>{filePath, pkIndex, startOffset},
csvStreamingReader{move(csvStreamingReader)} {};
std::unique_ptr<NodeCopyMorsel<arrow::Array>> getMorsel() override;

private:
std::shared_ptr<arrow::csv::StreamingReader> csvStreamingReader;
};

template<typename T>
class ParquetNodeCopySharedState : public NodeCopySharedState<T, arrow::ChunkedArray> {

public:
ParquetNodeCopySharedState(std::string filePath, HashIndexBuilder<T>* pkIndex,
common::offset_t startOffset, uint64_t numBlocks,
std::unique_ptr<parquet::arrow::FileReader> parquetReader)
: NodeCopySharedState<T, arrow::ChunkedArray>{filePath, pkIndex, startOffset},
numBlocks{numBlocks}, parquetReader{std::move(parquetReader)} {};
std::unique_ptr<NodeCopyMorsel<arrow::ChunkedArray>> getMorsel() override;

public:
uint64_t numBlocks;

private:
std::unique_ptr<parquet::arrow::FileReader> parquetReader;
};

class NodeCopier : public TableCopier {

public:
Expand All @@ -23,7 +131,7 @@ class NodeCopier : public TableCopier {
protected:
void initializeColumnsAndLists() override;

void populateColumnsAndLists() override;
void populateColumnsAndLists(processor::ExecutionContext* executionContext) override;

void saveToFile() override;

Expand All @@ -36,13 +144,15 @@ class NodeCopier : public TableCopier {

private:
template<typename T>
arrow::Status populateColumns();
arrow::Status populateColumns(processor::ExecutionContext* executionContext);

template<typename T>
arrow::Status populateColumnsFromCSV(std::unique_ptr<HashIndexBuilder<T>>& pkIndex);
arrow::Status populateColumnsFromCSV(processor::ExecutionContext* executionContext,
std::unique_ptr<HashIndexBuilder<T>>& pkIndex);

template<typename T>
arrow::Status populateColumnsFromParquet(std::unique_ptr<HashIndexBuilder<T>>& pkIndex);
arrow::Status populateColumnsFromParquet(processor::ExecutionContext* executionContext,
std::unique_ptr<HashIndexBuilder<T>>& pkIndex);

template<typename T>
static void putPropsOfLinesIntoColumns(InMemColumnChunk* columnChunk, NodeInMemColumn* column,
Expand All @@ -51,21 +161,9 @@ class NodeCopier : public TableCopier {
PageByteCursor& overflowCursor);

// Concurrent tasks.
// Note that primaryKeyPropertyIdx is *NOT* the property ID of the primary key property.
template<typename T1, typename T2>
static arrow::Status batchPopulateColumnsTask(uint64_t primaryKeyPropertyIdx, uint64_t blockIdx,
uint64_t startOffset, HashIndexBuilder<T1>* pkIndex, NodeCopier* copier,
const std::vector<std::shared_ptr<T2>>& batchColumns, std::string filePath);

template<typename T>
arrow::Status assignCopyCSVTasks(arrow::csv::StreamingReader* csvStreamingReader,
common::offset_t startOffset, std::string filePath,
std::unique_ptr<HashIndexBuilder<T>>& pkIndex);

template<typename T>
arrow::Status assignCopyParquetTasks(parquet::arrow::FileReader* parquetReader,
common::offset_t startOffset, std::string filePath,
std::unique_ptr<HashIndexBuilder<T>>& pkIndex);
static void batchPopulateColumnsTask(NodeCopySharedState<T1, T2>* sharedState,
NodeCopier* copier, processor::ExecutionContext* executionContext);

template<typename T>
static void appendPKIndex(InMemColumnChunk* chunk, InMemOverflowFile* overflowFile,
Expand Down
4 changes: 2 additions & 2 deletions src/include/storage/copier/npy_node_copier.h
Original file line number Diff line number Diff line change
Expand Up @@ -27,9 +27,9 @@ class NpyNodeCopier : public NodeCopier {
~NpyNodeCopier() override = default;

private:
void populateColumnsAndLists() override;
void populateColumnsAndLists(processor::ExecutionContext* executionContext) override;

void populateInMemoryStructures() override;
void populateInMemoryStructures(processor::ExecutionContext* executionContext) override;

void initializeNpyReaders();

Expand Down
2 changes: 1 addition & 1 deletion src/include/storage/copier/rel_copier.h
Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,7 @@ class RelCopier : public TableCopier {

void initializeColumnsAndLists() override;

void populateColumnsAndLists() override;
void populateColumnsAndLists(processor::ExecutionContext* executionContext) override;

void saveToFile() override;

Expand Down
13 changes: 4 additions & 9 deletions src/include/storage/copier/table_copier.h
Original file line number Diff line number Diff line change
Expand Up @@ -41,16 +41,16 @@ class TableCopier {

virtual ~TableCopier() = default;

uint64_t copy();
uint64_t copy(processor::ExecutionContext* executionContext);

protected:
virtual void initializeColumnsAndLists() = 0;

virtual void populateColumnsAndLists() = 0;
virtual void populateColumnsAndLists(processor::ExecutionContext* executionContext) = 0;

virtual void saveToFile() = 0;

virtual void populateInMemoryStructures();
virtual void populateInMemoryStructures(processor::ExecutionContext* executionContext);

inline void updateTableStatistics() {
tablesStatistics->setNumTuplesForTable(tableSchema->tableID, numRows);
Expand All @@ -65,13 +65,8 @@ class TableCopier {
arrow::Status initCSVReaderAndCheckStatus(
std::shared_ptr<arrow::csv::StreamingReader>& csv_streaming_reader,
const std::string& filePath);
arrow::Status initCSVReader(std::shared_ptr<arrow::csv::StreamingReader>& csv_streaming_reader,
const std::string& filePath);

arrow::Status initArrowReaderAndCheckStatus(
std::shared_ptr<arrow::ipc::RecordBatchFileReader>& ipc_reader,
const std::string& filePath);
arrow::Status initArrowReader(std::shared_ptr<arrow::ipc::RecordBatchFileReader>& ipc_reader,
arrow::Status initCSVReader(std::shared_ptr<arrow::csv::StreamingReader>& csv_streaming_reader,
const std::string& filePath);

arrow::Status initParquetReaderAndCheckStatus(
Expand Down
1 change: 1 addition & 0 deletions src/main/database.cpp
Original file line number Diff line number Diff line change
Expand Up @@ -27,6 +27,7 @@ SystemConfig::SystemConfig(uint64_t bufferPoolSize_) {
(double_t)std::min(systemMemSize, (std::uint64_t)UINTPTR_MAX));
}
bufferPoolSize = bufferPoolSize_;
auto maxConcurrency = std::thread::hardware_concurrency();
maxNumThreads = std::thread::hardware_concurrency();
}

Expand Down
4 changes: 2 additions & 2 deletions src/processor/operator/copy/copy_node.cpp
Original file line number Diff line number Diff line change
Expand Up @@ -15,11 +15,11 @@ uint64_t CopyNode::executeInternal(
if (copyDescription.fileType == common::CopyDescription::FileType::NPY) {
auto nodeCopier = std::make_unique<NpyNodeCopier>(copyDescription, wal->getDirectory(),
*taskScheduler, *catalog, tableID, nodesStatistics);
numNodesCopied = nodeCopier->copy();
numNodesCopied = nodeCopier->copy(executionContext);
} else {
auto nodeCopier = std::make_unique<NodeCopier>(copyDescription, wal->getDirectory(),
*taskScheduler, *catalog, tableID, nodesStatistics);
numNodesCopied = nodeCopier->copy();
numNodesCopied = nodeCopier->copy(executionContext);
}
for (auto& relTableSchema : catalog->getAllRelTableSchemasContainBoundTable(tableID)) {
relsStore.getRelTable(relTableSchema->tableID)
Expand Down
4 changes: 2 additions & 2 deletions src/processor/operator/copy/copy_rel.cpp
Original file line number Diff line number Diff line change
Expand Up @@ -9,9 +9,9 @@ namespace processor {

uint64_t CopyRel::executeInternal(
kuzu::common::TaskScheduler* taskScheduler, ExecutionContext* executionContext) {
auto relCSVCopier = make_unique<RelCopier>(copyDescription, wal->getDirectory(), *taskScheduler,
auto relCopier = make_unique<RelCopier>(copyDescription, wal->getDirectory(), *taskScheduler,
*catalog, nodesStore, executionContext->bufferManager, tableID, relsStatistics);
auto numRelsCopied = relCSVCopier->copy();
auto numRelsCopied = relCopier->copy(executionContext);
wal->logCopyRelRecord(tableID);
return numRelsCopied;
}
Expand Down
Loading