Percona xtrabackup restore [ERROR] --initialize specified but the data directory has files in it. Aborting

MySQL & MariaDB Percona XtraBackup
1

xtrabackup version: 2.4
mysql version: docker mysql5.7
step 1: backup

innobackupex --defaults-file=~/.my.cnf.bak --user=root --password="123456" --databases=kk --backup /data/backups/

step 2: start a new mysql

docker run -d --name=mysqltt -p 3307:3306 \
    -e TZ=Asia/Shanghai \
    -e MYSQL_ROOT_PASSWORD=123456 \
    -v /alidata1/mysql_multi/data3307/mydata:/var/lib/mysql \
    mysql:5.7 --character-set-server=utf8mb4 \
    --collation-server=utf8mb4_unicode_ci

step 3: apply-log

innobackupex --apply-log --redo-only /data/backups/2023-08-07_15-29-16/

step 4: restore

docker stop mysqltt

rm -rf /alidata1/mysql_multi/data3307/mydata/*

innobackupex --copy-back --datadir=/alidata1/mysql_multi/data3307/mydata/  /data/backups/2023-08-07_15-29-16/

step: start mysqltt

docker start mysqltt

the error

2023-08-07 16:04:18+08:00 [Note] [Entrypoint]: Entrypoint script for MySQL Server 5.7.36-1debian10 started.
2023-08-07 16:04:19+08:00 [Note] [Entrypoint]: Switching to dedicated user 'mysql'
2023-08-07 16:04:19+08:00 [Note] [Entrypoint]: Entrypoint script for MySQL Server 5.7.36-1debian10 started.
2023-08-07 16:04:19+08:00 [Note] [Entrypoint]: Initializing database files
2023-08-07T08:04:19.211882Z 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details).
2023-08-07T08:04:19.213398Z 0 [ERROR] --initialize specified but the data directory has files in it. Aborting.
2023-08-07T08:04:19.213431Z 0 [ERROR] Aborting
2

Hello seqwait,
As per the error log docker container is trying to start with a freshly created mysql directory and it’s trying to run mysqld --initialize

2023-08-07T08:04:19.213398Z 0 [ERROR] --initialize specified but the data directory has files in it. Aborting.

In entrypoint scipt i found these functions:

you may found script you have by
docker exec -ti mysqltt /bin/bash
and
cat entrypoint.sh


# initializes the database directory
docker_init_database_dir() {
	mysql_note "Initializing database files"
	"$@" --initialize-insecure --default-time-zone=SYSTEM
	mysql_note "Database files initialized"
}

and it should not be running if you have something in directory:

...
docker_setup_env() {
	# Get config
	declare -g DATADIR SOCKET
	DATADIR="$(mysql_get_config 'datadir' "$@")"
	SOCKET="$(mysql_get_config 'socket' "$@")"

	# Initialize values that might be stored in a file
	file_env 'MYSQL_ROOT_HOST' '%'
	file_env 'MYSQL_DATABASE'
	file_env 'MYSQL_USER'
	file_env 'MYSQL_PASSWORD'
	file_env 'MYSQL_ROOT_PASSWORD'

	declare -g DATABASE_ALREADY_EXISTS
	if [ -d "$DATADIR/mysql" ]; then
		DATABASE_ALREADY_EXISTS='true'
	fi
}
...
	if [ -z "$DATABASE_ALREADY_EXISTS" ]; then
			docker_verify_minimum_env

			# check dir permissions to reduce likelihood of half-initialized database
			ls /docker-entrypoint-initdb.d/ > /dev/null

			docker_init_database_dir "$@"

			mysql_note "Starting temporary server"
			docker_temp_server_start "$@"
			mysql_note "Temporary server started."

			mysql_socket_fix
			docker_setup_db
			docker_process_init_files /docker-entrypoint-initdb.d/*

			mysql_expire_root_user

			mysql_note "Stopping temporary server"
			docker_temp_server_stop
			mysql_note "Temporary server stopped"

			echo
			mysql_note "MySQL init process done. Ready for start up."
			echo
		else
			mysql_socket_fix
		fi
	fi
	exec "$@"

Could you please check if you have files in and also if mysql directory is there database

/alidata1/mysql_multi/data3307/mydata/

also you may inspect entrypoint.sh for more info

Regards,
Denis Subbota.
Managed Services, Percona.

3

Hello @seqwait,
innobackupex is an extremely old and dead tool. What modern documentation did you read to use this tool instead of xtrabackup?

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