Charts: [stable/mysql] --initialize specified but the data directory has files in it. Aborting.

[rim-wood]

Describe the bug
when i`m use cmd "helm install ", deployment is start error.
and i find the log

i`m modify the vaule.yaml

## mysql image version
## ref: https://hub.docker.com/r/library/mysql/tags/
##
image: "mysql"
imageTag: "5.7.28"

strategy:
  type: Recreate

busybox:
  image: "busybox"
  tag: "1.29.3"

testFramework:
  enabled: true
  image: "dduportal/bats"
  tag: "0.4.0"

## Specify password for root user
##
## Default: random 10 character string
mysqlRootPassword: 123456

## Create a database user
##
mysqlUser: nacos
## Default: random 10 character string
mysqlPassword: nacos

## Allow unauthenticated access, uncomment to enable
##
# mysqlAllowEmptyPassword: true

## Create a database
##
mysqlDatabase: nacos_devtest

## Specify an imagePullPolicy (Required)
## It's recommended to change this to 'Always' if the image tag is 'latest'
## ref: http://kubernetes.io/docs/user-guide/images/#updating-images
##
imagePullPolicy: IfNotPresent

## Additionnal arguments that are passed to the MySQL container.
## For example use --default-authentication-plugin=mysql_native_password if older clients need to
## connect to a MySQL 8 instance.
args: []

extraVolumes: |
  # - name: extras
  #   emptyDir: {}
extraVolumeMounts: |
  # - name: extras
  #   mountPath: /usr/share/extras
  #   readOnly: true
extraInitContainers: |
  # - name: do-something
  #   image: busybox
  #   command: ['do', 'something']
# Optionally specify an array of imagePullSecrets.
# Secrets must be manually created in the namespace.
# ref: https://kubernetes.io/docs/concepts/containers/images/#specifying-imagepullsecrets-on-a-pod
# imagePullSecrets:
  # - name: myRegistryKeySecretName

## Node selector
## ref: https://kubernetes.io/docs/concepts/configuration/assign-pod-node/#nodeselector
nodeSelector: {}

## Tolerations for pod assignment
## Ref: https://kubernetes.io/docs/concepts/configuration/taint-and-toleration/
##
tolerations: []

livenessProbe:
  initialDelaySeconds: 120
  periodSeconds: 10
  timeoutSeconds: 5
  successThreshold: 1
  failureThreshold: 3

readinessProbe:
  initialDelaySeconds: 5
  periodSeconds: 10
  timeoutSeconds: 1
  successThreshold: 1
  failureThreshold: 3

## Persist data to a persistent volume
persistence:
  enabled: true
  ## database data Persistent Volume Storage Class
  ## If defined, storageClassName: <storageClass>
  ## If set to "-", storageClassName: "", which disables dynamic provisioning
  ## If undefined (the default) or set to null, no storageClassName spec is
  ##   set, choosing the default provisioner.  (gp2 on AWS, standard on
  ##   GKE, AWS & OpenStack)
  ##
  storageClass: 
    storageClassName: nacos-sc-mysql
    provisioner: fuseim.pri/ifs
    classParameters: {}
  accessMode: ReadWriteOnce
  size: 10Gi
  annotations: {}

## Use an alternate scheduler, e.g. "stork".
## ref: https://kubernetes.io/docs/tasks/administer-cluster/configure-multiple-schedulers/
##
# schedulerName:

## Security context
securityContext:
  enabled: false
  runAsUser: 999
  fsGroup: 999

## Configure resource requests and limits
## ref: http://kubernetes.io/docs/user-guide/compute-resources/
##
resources:
  requests:
    memory: 2Gi
    cpu: 1000m

# Custom mysql configuration files path
configurationFilesPath: /etc/mysql/conf.d/

# Custom mysql configuration files used to override default mysql settings
configurationFiles: 
  mysql.cnf: |-
    [mysqld]
    pid-file  = /var/run/mysqld/mysqld.pid
    socket    = /var/run/mysqld/mysqld.sock
    datadir   = /var/lib/mysql

    symbolic-links=0

    secure-file-priv= NULL
    skip-host-cache

    skip-name-resolve



    server-id = 1

    port = 3306

    autocommit = 0


    character_set_server=utf8mb4


    collation-server = utf8mb4_general_ci


    init_connect='SET NAMES utf8mb4'


    transaction_isolation = READ-COMMITTED


    lower_case_table_names = 1


    max_connections = 800


    back_log = 210


    max_connect_errors = 1000


    explicit_defaults_for_timestamp = true


    max_allowed_packet = 128M


    interactive_timeout = 1800
    wait_timeout = 1800



    tmpdir  = /tmp


    tmp_table_size = 134217728
    max_heap_table_size = 134217728


    read_buffer_size = 8388608


    read_rnd_buffer_size = 2097152


    join_buffer_size = 8388608


    sort_buffer_size = 4194304


    binlog_cache_size = 524288



    log_error = /var/log/mysql/error.log


    slow_query_log = 1
    slow_query_log_file = /var/log/mysql/slow.log


    log_queries_not_using_indexes = 1


    log_throttle_queries_not_using_indexes = 5


    log_slow_slave_statements = 1


    long_query_time = 8


    min_examined_row_limit = 1000


    expire_logs_days = 7





    master_info_repository = TABLE
    relay_log_info_repository = TABLE


    log_bin = /var/log/mysql/bin.log

    sync_binlog = 5


    log_slave_updates = 1


    gtid_mode = on


    enforce_gtid_consistency = 1


    binlog_gtid_simple_recovery = 1


    log_slave_updates = 1


    binlog_format = row


    binlog_row_image = minimal


    relay_log = /var/log/mysql/relay.log


    relay_log_recovery = 1


    slave_skip_errors = ddl_exist_errors





    innodb_page_size = 16384


    innodb_buffer_pool_size = 2G


    innodb_buffer_pool_instances = 8


    innodb_buffer_pool_load_at_startup = 1

    innodb_buffer_pool_dump_at_shutdown = 1


    innodb_lru_scan_depth = 2000

    innodb_io_capacity = 4000


    innodb_io_capacity_max = 8000


    innodb_lock_wait_timeout = 30


    innodb_file_per_table = 1


    innodb_undo_logs = 128


    innodb_log_file_size = 1073741842
    innodb_log_buffer_size = 16777216


    innodb_purge_threads = 4


    innodb_thread_concurrency = 0


    innodb_print_all_deadlocks = 1

    innodb_sort_buffer_size = 8338608 
# Custom mysql init SQL files used to initialize the database
initializationFiles: 
  nacos-config.sql: |-
    use nacos_devtest;
    CREATE TABLE `config_info` (
      `id` bigint(20) NOT NULL AUTO_INCREMENT COMMENT 'id',
      `data_id` varchar(255) NOT NULL COMMENT 'data_id',
      `group_id` varchar(255) DEFAULT NULL,
      `content` longtext NOT NULL COMMENT 'content',
      `md5` varchar(32) DEFAULT NULL COMMENT 'md5',
      `gmt_create` datetime NOT NULL DEFAULT '2010-05-05 00:00:00' COMMENT '创建时间',
      `gmt_modified` datetime NOT NULL DEFAULT '2010-05-05 00:00:00' COMMENT '修改时间',
      `src_user` text COMMENT 'source user',
      `src_ip` varchar(20) DEFAULT NULL COMMENT 'source ip',
      `app_name` varchar(128) DEFAULT NULL,
      `tenant_id` varchar(128) DEFAULT '' COMMENT '租户字段',
      `c_desc` varchar(256) DEFAULT NULL,
      `c_use` varchar(64) DEFAULT NULL,
      `effect` varchar(64) DEFAULT NULL,
      `type` varchar(64) DEFAULT NULL,
      `c_schema` text,
      PRIMARY KEY (`id`),
      UNIQUE KEY `uk_configinfo_datagrouptenant` (`data_id`,`group_id`,`tenant_id`)
    ) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin COMMENT='config_info';
#  first-db.sql: |-
#    CREATE DATABASE IF NOT EXISTS first DEFAULT CHARACTER SET utf8 DEFAULT COLLATE utf8_general_ci;
#  second-db.sql: |-
#    CREATE DATABASE IF NOT EXISTS second DEFAULT CHARACTER SET utf8 DEFAULT COLLATE utf8_general_ci;

metrics:
  enabled: false
  image: prom/mysqld-exporter
  imageTag: v0.10.0
  imagePullPolicy: IfNotPresent
  resources: {}
  annotations: {}
    # prometheus.io/scrape: "true"
    # prometheus.io/port: "9104"
  livenessProbe:
    initialDelaySeconds: 15
    timeoutSeconds: 5
  readinessProbe:
    initialDelaySeconds: 5
    timeoutSeconds: 1
  flags: []
  serviceMonitor:
    enabled: false
    additionalLabels: {}

## Configure the service
## ref: http://kubernetes.io/docs/user-guide/services/
service:
  annotations: {}
  ## Specify a service type
  ## ref: https://kubernetes.io/docs/concepts/services-networking/service/#publishing-services---service-types
  type: ClusterIP
  port: 3306
  # nodePort: 32000
  # loadBalancerIP:

## Pods Service Account
## ref: https://kubernetes.io/docs/tasks/configure-pod-container/configure-service-account/
serviceAccount:
  ## Specifies whether a ServiceAccount should be created
  ##
  create: false
  ## The name of the ServiceAccount to use.
  ## If not set and create is true, a name is generated using the mariadb.fullname template
  # name:

ssl:
  enabled: false
  secret: mysql-ssl-certs
  certificates:
#  - name: mysql-ssl-certs
#    ca: |-
#      -----BEGIN CERTIFICATE-----
#      ...
#      -----END CERTIFICATE-----
#    cert: |-
#      -----BEGIN CERTIFICATE-----
#      ...
#      -----END CERTIFICATE-----
#    key: |-
#      -----BEGIN RSA PRIVATE KEY-----
#      ...
#      -----END RSA PRIVATE KEY-----

## Populates the 'TZ' system timezone environment variable
## ref: https://dev.mysql.com/doc/refman/5.7/en/time-zone-support.html
##
## Default: nil (mysql will use image's default timezone, normally UTC)
## Example: 'Australia/Sydney'
# timezone:

# Deployment Annotations
deploymentAnnotations: {}

# To be added to the database server pod(s)
podAnnotations: {}
podLabels: {}

## Set pod priorityClassName
# priorityClassName: {}


## Init container resources defaults
initContainer:
  resources:
    requests:
      memory: 10Mi
      cpu: 10m

and i add the storageclass.yaml

{{- if and .Values.persistence.enabled (not .Values.persistence.existingClaim) -}}
apiVersion: storage.k8s.io/v1
kind: StorageClass
metadata:
   name: {{ .Values.persistence.storageClass.storageClassName }}
provisioner: 
{{ toYaml .Values.persistence.storageClass.provisioner | indent 2 }}
parameters:
{{ toYaml .Values.persistence.storageClass.classParameters | indent 2 }}
reclaimPolicy: Retain
allowVolumeExpansion: true
{{- end }}

I found the same error because of the lost + found folder
290
Or data exists in the mounted host folder
398

But my error is not like this，In the deployment.yaml file, initC is defined and lost + found is deleted and i'm user the storageclass create the pvc+pv，so pv is empty.

and the pod was first created，these files are created below my pv ，

Then the pod reports an error
Version of Helm and Kubernetes:
v1.13.5

Which chart:
https://hub.helm.sh/charts/stable/mysql

[rim-wood]

One more thing to add：

modify the pvc.yaml：

{{- if and .Values.persistence.enabled (not .Values.persistence.existingClaim) }}
kind: PersistentVolumeClaim
apiVersion: v1
metadata:
  name: {{ template "mysql.fullname" . }}
  namespace: {{ .Release.Namespace }}
{{- with .Values.persistence.annotations  }}
  annotations:
{{ toYaml . | indent 4 }}
{{- end }}
  labels:
    app: {{ template "mysql.fullname" . }}
    chart: "{{ .Chart.Name }}-{{ .Chart.Version }}"
    release: "{{ .Release.Name }}"
    heritage: "{{ .Release.Service }}"
spec:
  accessModes:
    - {{ .Values.persistence.accessMode | quote }}
  resources:
    requests:
      storage: {{ .Values.persistence.size | quote }}
{{- if .Values.persistence.storageClass }}
{{- if (eq "-" .Values.persistence.storageClass.storageClassName) }}
  storageClassName: ""
{{- else }}
  storageClassName: "{{ .Values.persistence.storageClass.storageClassName }}"
{{- end }}
{{- end }}
{{- end }}

[one-two-my-gad]

helm lint 试过么

[rim-wood]

helm lint 试过么

能创建成功，helm lint只是校验文件格式的。

我的错误时pod里面的mysql初始化时，说数据文件夹中有数据

[one-two-my-gad]

头盔皮棉试过么

能创造成功，helm lint只是校验文件格式的。

我的错误时pod里面的mysql初始化时，说数据文件夹中有数据

方便发下部署命令么

[dacianmujdar]

I'm having the same issue. Any luck solving it?

[rim-wood]

I'm having the same issue. Any luck solving it?

no，i have given up，if you solved，please tell me the way

[stale[bot]]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Any further update will cause the issue/pull request to no longer be considered stale. Thank you for your contributions.

[stale[bot]]

This issue is being automatically closed due to inactivity.

[rim-wood]

hello everybody，i have been resolved this error.The reason is nfs server，but i don·t know why. I just used the hostpath pv to replace storageclass.

[chrouzz]

same issue here

[avnertzur]

Adding the below solved my issue
args:
- "--ignore-db-dir=lost+found"

[mrandrewdh]

Adding the below solved my issue
args:

• "--ignore-db-dir=lost+found"

Where abouts did you add this argument exactly? I'm having this issue when trying to mount an external volume with mysql...thanks!

[avnertzur]

Adding the below solved my issue
args:

• "--ignore-db-dir=lost+found"

Where abouts did you add this argument exactly? I'm having this issue when trying to mount an external volume with mysql...thanks!

I'm using helm chart, so in the Deployment template I added the "args" as below:

          args:
            - "--ignore-db-dir=lost+found"
          volumeMounts:
            - name: mysql-initdb
              mountPath: /docker-entrypoint-initdb.d
            - name: {{ .Values.Mysql.name }}-persistent-storage
              mountPath: /var/lib/mysql

[ricardoandre97]

Adding the below solved my issue
args:

• "--ignore-db-dir=lost+found"

This is it!

[294434171]

Adding the below solved my issue
args:

• "--ignore-db-dir=lost+found"

Where abouts did you add this argument exactly? I'm having this issue when trying to mount an external volume with mysql...thanks!

I'm using helm chart, so in the Deployment template I added the "args" as below:

          args:
            - "--ignore-db-dir=lost+found"
          volumeMounts:
            - name: mysql-initdb
              mountPath: /docker-entrypoint-initdb.d
            - name: {{ .Values.Mysql.name }}-persistent-storage
              mountPath: /var/lib/mysql

This solution is working on OpenShift 4.5, thanks