Concurrent flush on Appender triggers corrupt row

[paulsputer]

Using the Appender I can write from multiple go routines perfectly fine. However, when I set up a ticker to call Flush at a regular interval it appears a race condition is created that materialises with the following error following error:

database/sql/driver: could not flush appender: duckdb error: PRIMARY KEY or UNIQUE constraint violated: duplicate key "80000000-0000-0000-0000-000000000000": appended data has been invalidated due to corrupt row

My reason for calling Flush on a regular basis is to minimise the risk of data loss in the event of a process or system issue. Where it does occur I would like to be able to quantify the level of data loss ie. "30 seconds of data".

the documentation mentions that concurrency works in a single process which this is:

DuckDB supports concurrency within a single process according to the following rules. As long as there are no write conflicts, multiple concurrent writes will succeed. Appends will never conflict, even on the same table.

If I surround all calls to Append and Flush with a calls to Lock and Unlock for a sync.Mutex it operates fine. Though this would then seem cancel out the concurrent benefits. While in my use-case I can switch to a channel. It seems like something that could impact many other users. Digging into the C implementation of the Appender I can't seem to find any race protection there.

Happy to look into contributing a PR to fix but keen to scope this out, is this a feature/use-case that simply needs a little extra documentation, or a bug where a fix maybe either a lower level use of a mutex or a SafeFlush function be added?

Environment

Replicated on: iOS, Linux
Go-DuckDB: v1.8.3
DuckDB: v1.0.0 1f98600c2c

Replication

The following code sample can be used to replicate

package main

import (
	"context"
	"database/sql/driver"
	"fmt"
	"sync"
	"time"

	"github.com/gofrs/uuid/v5"
	"github.com/marcboeker/go-duckdb"
)

func main() {

	fmt.Println("Start")
	db := NewDuckDb()

	db.RunEventLoop()

	wg := &sync.WaitGroup{}
	asyncAppend(db, 1, wg)
	asyncAppend(db, 2, wg)
	asyncAppend(db, 3, wg)

	wg.Wait()

	fmt.Println("End")
}

func asyncAppend(db *DuckDbAppender, id int, wg *sync.WaitGroup) {

	wg.Add(1)

	go func() {
		for i := 0; i < 1000; i++ {
			db.Append(uuid.Must(uuid.NewV4()), time.Now(), fmt.Sprintf("row from routine %d iteration %d", id, i))
			time.Sleep(time.Millisecond * 20)
		}
		wg.Done()
	}()

}

type DuckDbAppender struct {
	ddb    *duckdb.Connector
	con    driver.Conn
	app    *duckdb.Appender
	ticker *time.Ticker
}

func NewDuckDb() *DuckDbAppender {
	dbFilepath := "test.duckdb"
	tableName := "test"
	schema := `CREATE TABLE IF NOT EXISTS test (
				request_id uuid PRIMARY KEY DEFAULT gen_random_uuid(),
				created_at TIMESTAMP NOT NULL DEFAULT CURRENT_TIMESTAMP,
				description varchar(255) NULL
			);`

	o := &DuckDbAppender{
		ticker: time.NewTicker(time.Second * 5),
	}

	var err error

	o.ddb, err = duckdb.NewConnector(fmt.Sprintf("%s?threads=1", dbFilepath), func(execer driver.ExecerContext) error {

		_, err := execer.ExecContext(context.TODO(), schema, nil)

		if err != nil {
			panic(fmt.Errorf("unexpected error executing connection query: %w", err))
		}

		return nil
	})

	o.con, err = o.ddb.Connect(context.TODO())

	if err != nil {
		panic(fmt.Errorf("unexpected error while connecting: %w", err))
	}

	o.app, err = duckdb.NewAppenderFromConn(o.con, "", tableName)

	if err != nil {
		panic(fmt.Errorf("unexpected error while connecting: %w", err))
	}

	return o
}

func (o *DuckDbAppender) RunEventLoop() {

	go func() {
		for {
			select {
			case <-o.ticker.C:
				{
					err := o.app.Flush()

					if err != nil {
						panic(fmt.Errorf("unexpected error while flushing: %w", err))
					}
				}
			}
		}

	}()
}

func (o *DuckDbAppender) Append(id uuid.UUID, date time.Time, desc string) error {
	err := o.app.AppendRow(
		duckdb.UUID(id),
		date,
		desc,
	)

	return err
}

[taniabogatsch]

Hi @paulsputer, thanks for raising this.

This is likely the same issue as duckdb/duckdb-rs#331 (comment).

My guess is that this is not an Appender issue, as the reproduction in the related issue does not use the Appender. More likely, gen_random_uuid() might not be concurrency safe.

[paulsputer]

Thanks @taniabogatsch wasn't aware of that issue with gen_random_uuid. I think in this case that's a symptom not a cause.

Thought process being that uuids in this reproduction are generated in Go, so the SQL default clause should never be triggered. However, the fact that it is would imply the chunk is somehow null for the uuid and so triggering gen_random_uuid.

My guess is that this is not an Appender issue, as the reproduction in the related issue does not use the Appender

To be sure the example is calling the AppendRow on a duckdb.Appender. Am I missing something?

Given the gen_random_uuid issue I've tweaked the reproduction to use a simple int instead. The error this time is

panic: unexpected error while flushing: database/sql/driver: could not flush appender: duckdb error: PRIMARY KEY or UNIQUE constraint violated: duplicate key "0": appended data has been invalidated due to corrupt row

Note that in this updated reproduction no call is being made to append 0

package main

import (
	"context"
	"database/sql/driver"
	"fmt"
	"sync"
	"time"

	"github.com/marcboeker/go-duckdb"
)

func main() {

	fmt.Println("Start")
	db := NewDuckDb()

	db.RunEventLoop()

	wg := &sync.WaitGroup{}
	asyncAppend(db, 1, wg, 1)
	asyncAppend(db, 2, wg, 5000)

	wg.Wait()

	fmt.Println("End")
}

func asyncAppend(db *DuckDbAppender, id int, wg *sync.WaitGroup, offset int) {

	wg.Add(1)

	go func() {
		for i := 0; i < 1000; i++ {
			db.Append(offset+i, time.Now(), fmt.Sprintf("row from routine %d iteration %d", id, i))
			time.Sleep(time.Millisecond * 20)
		}
		wg.Done()
	}()

}

type DuckDbAppender struct {
	ddb    *duckdb.Connector
	con    driver.Conn
	app    *duckdb.Appender
	ticker *time.Ticker
}

func NewDuckDb() *DuckDbAppender {
	dbFilepath := "test.duckdb"
	tableName := "test"
	schema := `CREATE TABLE IF NOT EXISTS test (
		id INTEGER PRIMARY KEY,
		created_at TIMESTAMP NOT NULL DEFAULT CURRENT_TIMESTAMP,
		description varchar(255) NULL
	);`

	o := &DuckDbAppender{
		ticker: time.NewTicker(time.Second * 5),
	}

	var err error

	o.ddb, err = duckdb.NewConnector(fmt.Sprintf("%s?threads=1", dbFilepath), func(execer driver.ExecerContext) error {

		_, err := execer.ExecContext(context.TODO(), schema, nil)

		if err != nil {
			panic(fmt.Errorf("unexpected error executing connection query: %w", err))
		}

		return nil
	})

	o.con, err = o.ddb.Connect(context.TODO())

	if err != nil {
		panic(fmt.Errorf("unexpected error while connecting: %w", err))
	}

	o.app, err = duckdb.NewAppenderFromConn(o.con, "", tableName)

	if err != nil {
		panic(fmt.Errorf("unexpected error while connecting: %w", err))
	}

	return o
}

func (o *DuckDbAppender) RunEventLoop() {

	go func() {
		for {
			select {
			case <-o.ticker.C:
				{
					err := o.app.Flush()

					if err != nil {
						panic(fmt.Errorf("unexpected error while flushing: %w", err))
					}
				}
			}
		}

	}()
}

func (o *DuckDbAppender) Append(id int, date time.Time, desc string) error {

	err := o.app.AppendRow(
		id,
		date,
		desc,
	)

	return err
}

[taniabogatsch]

Thought process being that uuids in this reproduction are generated in Go, so the SQL default clause should never be triggered. However, the fact that it is would imply the chunk is somehow null for the uuid and so triggering gen_random_uuid.

Oh yeah, I missed that!

Looking at your updated example again, this is happening on the go-duckdb side, as the Appender is not concurrency-safe. The calls below require multiple data chunks to be filled out concurrently, which is not supported. Also, flushing while still writing with AppendRow is not supported... 🤔

	asyncAppend(db, 1, wg, 1)
	asyncAppend(db, 2, wg, 5000)