Details
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Bug
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Status: Open (View Workflow)
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Major
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Resolution: Unresolved
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None
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None
Description
We installed the galera cluster using the bitnami mariadb-helm charts.
Affected Version 10.7.7 (not able to select it through the select field above)
After a while (few days) we always see deadlocks in the logs:
Caused by: java.sql.SQLException: (conn=371621) Lock wait timeout exceeded; try restarting transaction
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The values.yaml file:
image:
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tag: 10.7.7-debian-11-r30
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podAnnotations:
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vault.security.banzaicloud.io/vault-addr: "http://censored-for-compliance-reasons.com"
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vault.security.banzaicloud.io/vault-skip-verify: "true"
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vault.security.banzaicloud.io/vault-role: "cluster-nonprod"
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vault.security.banzaicloud.io/vault-path: "cluster-nonprod"
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serviceAccount:
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create: true
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automountServiceAccountToken: true
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fullnameOverride: dev-mariadb
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rbac:
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create: true
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podManagementPolicy: Parallel
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replicaCount: 3
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db:
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user: technical
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name: ""
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persistence:
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size: 20Gi
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usePasswordFiles: true
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customPasswordFiles:
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root: "/vault-secrets/rootpassword"
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user: "/vault-secrets/userpassword"
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mariabackup: "/vault-secrets/mariabackuppassword"
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extraVolumes:
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- name: vault-secrets-volume
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emptyDir: {}
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extraVolumeMounts:
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- mountPath: /vault-secrets
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name: vault-secrets-volume
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initContainers:
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- command:
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- bash
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- -c
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- |
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echo -n "$PASSWORD" > /vault-secrets/userpassword
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echo -n "$ROOTPASSWORD" > /vault-secrets/rootpassword
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echo -n "$MARIABACKUPPASSWORD" > /vault-secrets/mariabackuppassword
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image: ubuntu:jammy
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name: init-container
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volumeMounts:
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- mountPath: /vault-secrets
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name: vault-secrets-volume
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env:
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- name: PASSWORD
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value: vault:cluster-nonprod/data/dev/common/mariadb-galera/credentials#mariadb-password
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- name: ROOTPASSWORD
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value: vault:cluster-nonprod/data/dev/common/mariadb-galera/credentials#mariadb-root-password
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- name: MARIABACKUPPASSWORD
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value: vault:cluster-nonprod/data/dev/common/mariadb-galera/credentials#mariadb-galera-mariabackup-password
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resources:
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requests:
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cpu: 0.5
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memory: 4096Mi
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limits:
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cpu: 2
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memory: 4096Mi
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initdbScripts:
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init_dbs.sql: |
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CREATE DATABASE IF NOT EXISTS vault;
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CREATE DATABASE IF NOT EXISTS vault_lock;
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CREATE DATABASE IF NOT EXISTS keycloak;
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mariadbConfiguration: |-
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[client]
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port=3306
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socket=/opt/bitnami/mariadb/tmp/mysql.sock
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plugin_dir=/opt/bitnami/mariadb/plugin
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[mysqld]
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default_storage_engine=InnoDB
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basedir=/opt/bitnami/mariadb
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datadir=/bitnami/mariadb/data
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plugin_dir=/opt/bitnami/mariadb/plugin
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tmpdir=/opt/bitnami/mariadb/tmp
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socket=/opt/bitnami/mariadb/tmp/mysql.sock
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pid_file=/opt/bitnami/mariadb/tmp/mysqld.pid
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bind_address=0.0.0.0
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## Character set
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##
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collation_server=utf8_unicode_ci
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init_connect='SET NAMES utf8'
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character_set_server=utf8
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## MyISAM
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##
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key_buffer_size=32M
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myisam_recover_options=FORCE,BACKUP
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## Safety
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##
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skip_host_cache
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skip_name_resolve
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max_allowed_packet=16M
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max_connect_errors=1000000
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sql_mode=IGNORE_SPACE,ONLY_FULL_GROUP_BY,STRICT_TRANS_TABLES,NO_ZERO_IN_DATE,NO_ZERO_DATE,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION
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sysdate_is_now=1
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## Binary Logging
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##
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log_bin=mysql-bin
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expire_logs_days=14
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# Disabling for performance per http://severalnines.com/blog/9-tips-going-production-galera-cluster-mysql
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sync_binlog=0
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# Required for Galera
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binlog_format=row
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## Caches and Limits
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##
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tmp_table_size=32M
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max_heap_table_size=32M
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# Re-enabling as now works with Maria 10.1.2
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query_cache_type=1
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query_cache_limit=4M
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query_cache_size=256M
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max_connections=500
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thread_cache_size=50
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open_files_limit=65535
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table_definition_cache=4096
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table_open_cache=4096
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## InnoDB
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##
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innodb=FORCE
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innodb_strict_mode=1
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# Mandatory per https://github.com/codership/documentation/issues/25
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innodb_autoinc_lock_mode=2
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# Per https://www.percona.com/blog/2006/08/04/innodb-double-write/
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innodb_doublewrite=1
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innodb_flush_method=O_DIRECT
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innodb_log_files_in_group=2
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innodb_log_file_size=128M
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innodb_flush_log_at_trx_commit=1
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innodb_file_per_table=1
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# 80% Memory is default reco.
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# Need to re-evaluate when DB size grows
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innodb_buffer_pool_size=2G
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innodb_file_format=Barracuda
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## Logging
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##
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log_error=/opt/bitnami/mariadb/logs/mysqld.log
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slow_query_log_file=/opt/bitnami/mariadb/logs/mysqld.log
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log_queries_not_using_indexes=1
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slow_query_log=1
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[galera]
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wsrep_on=ON
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wsrep_provider=/opt/bitnami/mariadb/lib/libgalera_smm.so
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wsrep_sst_method=mariabackup
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wsrep_slave_threads=4
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wsrep_cluster_address=gcomm://
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wsrep_cluster_name=galera
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wsrep_sst_auth="root:"
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# Enabled for performance per https://mariadb.com/kb/en/innodb-system-variables/#innodb_flush_log_at_trx_commit
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innodb_flush_log_at_trx_commit=2
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# MYISAM REPLICATION SUPPORT #
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wsrep_mode=REPLICATE_MYISAM
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[mariadb]
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plugin_load_add=auth_pam
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diagnosticMode:
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enabled: false
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We checked the nodes for there state and we saw that node dev-mariadb-0 has a process in "Waiting for certification" that never ends:
| 370905 | root | localhost | anonym | Query | 140221 | Waiting for certification | INSERT INTO `ACT_RU_VARIABLE` VALUES ('0018a8dc-afc8-11ee-8401-d2c062af09ed',1,'string','temporaryRa | 0.000 |
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It seems all the other processes waiting for this one to complete.
We have tried to kill this process, but a KILL 370905 just ends up with an additional process waiting for the one to complete.
We are only able to fix this problem by restarting the node again. The other both nodes working as expected and read and write is possible.
Any idea how to fix this problem, or how we are able to ensure that this didn`t happen again?
Additional Information
Full Processlist of node0:
MariaDB [(none)]> show processlist;
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+--------+-------------+-------------------+---------+------------+---------+---------------------------------+------------------------------------------------------------------------------------------------------+----------+
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| Id | User | Host | db | Command | Time | State | Info | Progress |
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+--------+-------------+-------------------+---------+------------+---------+---------------------------------+------------------------------------------------------------------------------------------------------+----------+
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| 1 | system user | | NULL | Sleep | 1977667 | wsrep aborter idle | NULL | 0.000 |
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| 2 | system user | | NULL | Sleep | 140221 | Waiting for TOI DDL | update ACT_RU_EXECUTION set
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REV_ = 2,
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PROC_DEF_ID_ = 'd5618a2e-9aa3-11ee-84ad-06434dd3b4 | 0.000 |
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| 7 | system user | | NULL | Sleep | 140674 | After apply log event | NULL | 0.000 |
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| 8 | system user | | NULL | Sleep | 140665 | After apply log event | NULL | 0.000 |
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| 9 | system user | | NULL | Sleep | 140681 | After apply log event | NULL | 0.000 |
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| 370905 | root | localhost | anonym | Query | 140221 | Waiting for certification | INSERT INTO `ACT_RU_VARIABLE` VALUES
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('0018a8dc-afc8-11ee-8401-d2c062af09ed',1,'string','temporaryRa | 0.000 |
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| 370942 | root | localhost | NULL | Query | 140044 | Waiting to execute in isolation | DROP DATABASE anonym | 0.000 |
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| 371448 | root | localhost | NULL | Query | 137554 | Waiting to execute in isolation | DROP DATABASE anonym | 0.000 |
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| 371473 | root | localhost | NULL | Query | 137424 | Waiting to execute in isolation | DROP DATABASE anonym | 0.000 |
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| 371585 | root | localhost | NULL | Query | 136880 | Waiting to execute in isolation | KILL QUERY 370942 | 0.000 |
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| 371619 | root | 10.42.1.163:57406 | anonym | Query | 135847 | starting | COMMIT | 0.000 |
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| 377012 | root | 10.42.1.163:45958 | anonym | Query | 108463 | starting | COMMIT | 0.000 |
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| 397698 | root | localhost | NULL | Query | 10473 | Waiting to execute in isolation | KILL QUERY 397677 | 0.000 |
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| 397701 | root | localhost | NULL | Query | 10429 | Waiting to execute in isolation | CREATE DATABASE test | 0.000 |
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| 398502 | root | localhost | anonym | Field List | 6647 | Waiting for table flush | NULL | 0.000 |
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| 398522 | root | localhost | NULL | Sleep | 6570 | | NULL | 0.000 |
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| 399845 | root | 10.42.0.36:45956 | anonym | Sleep | 285 | | NULL | 0.000 |
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| 399846 | root | 10.42.0.36:46010 | anonym | Sleep | 285 | | NULL | 0.000 |
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| 399883 | root | localhost | NULL | Query | 0 | starting | show processlist | 0.000 |
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+--------+-------------+-------------------+---------+------------+---------+---------------------------------+------------------------------------------------------------------------------------------------------+----------+
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20 rows in set (0.000 sec)
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I checked all the nodes for the status
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Node0:
MariaDB [(none)]> SHOW GLOBAL STATUS LIKE 'wsrep_%';
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+-------------------------------+------------------------------------
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| Variable_name | Value
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| wsrep_local_state_uuid | a11a7c71-9843-11ee-bf01-3e8006b3a5a5
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| wsrep_protocol_version | 10
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| wsrep_last_committed | 7458
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| wsrep_replicated | 1034
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| wsrep_replicated_bytes | 85241264
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| wsrep_repl_keys | 160959
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| wsrep_repl_keys_bytes | 1312816
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| wsrep_repl_data_bytes | 83857720
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| wsrep_repl_other_bytes | 0
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| wsrep_received | 3771
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| wsrep_received_bytes | 854031936
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| wsrep_local_commits | 753
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| wsrep_local_cert_failures | 0
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| wsrep_local_replays | 0
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| wsrep_local_send_queue | 0
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| wsrep_local_send_queue_max | 2
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| wsrep_local_send_queue_min | 0
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| wsrep_local_send_queue_avg | 0.000679348
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| wsrep_local_recv_queue | 9
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| wsrep_local_recv_queue_max | 9
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| wsrep_local_recv_queue_min | 0
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| wsrep_local_recv_queue_avg | 0.0285714
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| wsrep_local_cached_downto | 7143
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| wsrep_flow_control_paused_ns | 0
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| wsrep_flow_control_paused | 0
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| wsrep_flow_control_sent | 0
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| wsrep_flow_control_recv | 0
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| wsrep_flow_control_active | false
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| wsrep_flow_control_requested | false
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| wsrep_cert_deps_distance | 20.7702
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| wsrep_apply_oooe | 0.0141204
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| wsrep_apply_oool | 0.00347222
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| wsrep_apply_window | 1.04051
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| wsrep_apply_waits | 225
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| wsrep_commit_oooe | 0
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| wsrep_commit_oool | 0
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| wsrep_commit_window | 1.00834
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| wsrep_local_state | 4
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| wsrep_local_state_comment | Synced
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| wsrep_cert_index_size | 3781
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| wsrep_causal_reads | 0
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| wsrep_cert_interval | 15.1052
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| wsrep_open_transactions | 3
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| wsrep_open_connections | 7
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| wsrep_incoming_addresse | 10.42.1.156:0,10.42.6.39:0,10.42.17.43:0
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| wsrep_cluster_weight | 3
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| wsrep_desync_count | 1
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| wsrep_evs_delayed |
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| wsrep_evs_evict_list |
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| wsrep_evs_repl_latency | 0/0/0/0/0
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| wsrep_evs_state | OPERATIONAL
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| wsrep_gcomm_uuid | b123cdcc-9f46-11ee-924e-b2b1bdb1b017
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| wsrep_gmcast_segment | 0
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| wsrep_applier_thread_count | 4
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| wsrep_cluster_capabilities |
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| wsrep_cluster_conf_id | 27
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| wsrep_cluster_size | 3
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| wsrep_cluster_state_uui | a11a7c71-9843-11ee-bf01-3e8006b3a5a5
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| wsrep_cluster_status | Primary
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| wsrep_connected | ON
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| wsrep_local_bf_aborts | 0
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| wsrep_local_index | 1
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| wsrep_provider_capabilities | :MULTI_MASTER:CERTIFICATION:PARALLEL_APPLYING:TRX_REPLAY:ISOLATION:PAUSE:CAUSAL_READS:INCREMENTAL_WRITESET:UNORDERED:PREORDERED:STREAMING:NBO: |
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| wsrep_provider_name | Galera
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| wsrep_provider_vendor | Codership Oy <info@codership.com>
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| wsrep_provider_version | 4.13(r0f7af31)
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| wsrep_ready | ON
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| wsrep_rollbacker_thread_count | 1
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| wsrep_thread_count | 5
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69 rows in set (0.001 sec)
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Node1:
MariaDB [(none)]> SHOW GLOBAL STATUS LIKE 'wsrep_%';
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+-------------------------------+------------------------------------------------------------------------------------------------------------------------------------------------+
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| Variable_name | Value |
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+-------------------------------+------------------------------------------------------------------------------------------------------------------------------------------------+
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| wsrep_local_state_uuid | a11a7c71-9843-11ee-bf01-3e8006b3a5a5 |
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| wsrep_protocol_version | 10 |
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| wsrep_last_committed | 7480 |
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| wsrep_replicated | 1 |
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| wsrep_replicated_bytes | 464 |
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| wsrep_repl_keys | 1 |
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| wsrep_repl_keys_bytes | 32 |
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| wsrep_repl_data_bytes | 362 |
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| wsrep_repl_other_bytes | 0 |
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| wsrep_received | 19 |
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| wsrep_received_bytes | 14723 |
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| wsrep_local_commits | 0 |
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| wsrep_local_cert_failures | 0 |
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| wsrep_local_replays | 0 |
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| wsrep_local_send_queue | 0 |
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| wsrep_local_send_queue_max | 1 |
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| wsrep_local_send_queue_min | 0 |
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| wsrep_local_send_queue_avg | 0 |
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| wsrep_local_recv_queue | 0 |
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| wsrep_local_recv_queue_max | 1 |
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| wsrep_local_recv_queue_min | 0 |
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| wsrep_local_recv_queue_avg | 0 |
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| wsrep_local_cached_downto | 7454 |
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| wsrep_flow_control_paused_ns | 0 |
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| wsrep_flow_control_paused | 0 |
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| wsrep_flow_control_sent | 0 |
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| wsrep_flow_control_recv | 0 |
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| wsrep_flow_control_active | false |
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| wsrep_flow_control_requested | false |
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| wsrep_cert_deps_distance | 1.21053 |
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| wsrep_apply_oooe | 0 |
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| wsrep_apply_oool | 0 |
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| wsrep_apply_window | 1 |
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| wsrep_apply_waits | 0 |
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| wsrep_commit_oooe | 0 |
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| wsrep_commit_oool | 0 |
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| wsrep_commit_window | 1 |
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| wsrep_local_state | 4 |
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| wsrep_local_state_comment | Synced |
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| wsrep_cert_index_size | 3785 |
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| wsrep_causal_reads | 0 |
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| wsrep_cert_interval | 4323.37 |
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| wsrep_open_transactions | 0 |
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| wsrep_open_connections | 0 |
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| wsrep_incoming_addresses | 10.42.4.127:0,10.42.17.60:0,10.42.6.39:0 |
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| wsrep_cluster_weight | 3 |
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| wsrep_desync_count | 0 |
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| wsrep_evs_delayed | |
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| wsrep_evs_evict_list | |
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| wsrep_evs_repl_latency | 0/0/0/0/0 |
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| wsrep_evs_state | OPERATIONAL |
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| wsrep_gcomm_uuid | 499450f3-affe-11ee-aab6-9f2e869c0a93 |
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| wsrep_gmcast_segment | 0 |
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| wsrep_applier_thread_count | 4 |
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| wsrep_cluster_capabilities | |
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| wsrep_cluster_conf_id | 33 |
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| wsrep_cluster_size | 3 |
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| wsrep_cluster_state_uuid | a11a7c71-9843-11ee-bf01-3e8006b3a5a5 |
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| wsrep_cluster_status | Primary |
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| wsrep_connected | ON |
|
| wsrep_local_bf_aborts | 0 |
|
| wsrep_local_index | 1 |
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| wsrep_provider_capabilities | :MULTI_MASTER:CERTIFICATION:PARALLEL_APPLYING:TRX_REPLAY:ISOLATION:PAUSE:CAUSAL_READS:INCREMENTAL_WRITESET:UNORDERED:PREORDERED:STREAMING:NBO: |
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| wsrep_provider_name | Galera |
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| wsrep_provider_vendor | Codership Oy <info@codership.com> |
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| wsrep_provider_version | 4.13(r0f7af31) |
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| wsrep_ready | ON |
|
| wsrep_rollbacker_thread_count | 1 |
|
| wsrep_thread_count | 5 |
|
+-------------------------------+------------------------------------------------------------------------------------------------------------------------------------------------+
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69 rows in set (0.002 sec)
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Node2:
MariaDB [(none)]> SHOW GLOBAL STATUS LIKE 'wsrep_%';
|
+-------------------------------+------------------------------------------------------------------------------------------------------------------------------------------------+
|
| Variable_name | Value |
|
+-------------------------------+------------------------------------------------------------------------------------------------------------------------------------------------+
|
| wsrep_local_state_uuid | a11a7c71-9843-11ee-bf01-3e8006b3a5a5 |
|
| wsrep_protocol_version | 10 |
|
| wsrep_last_committed | 7480 |
|
| wsrep_replicated | 1 |
|
| wsrep_replicated_bytes | 456 |
|
| wsrep_repl_keys | 1 |
|
| wsrep_repl_keys_bytes | 32 |
|
| wsrep_repl_data_bytes | 360 |
|
| wsrep_repl_other_bytes | 0 |
|
| wsrep_received | 12 |
|
| wsrep_received_bytes | 13784 |
|
| wsrep_local_commits | 0 |
|
| wsrep_local_cert_failures | 0 |
|
| wsrep_local_replays | 0 |
|
| wsrep_local_send_queue | 0 |
|
| wsrep_local_send_queue_max | 1 |
|
| wsrep_local_send_queue_min | 0 |
|
| wsrep_local_send_queue_avg | 0 |
|
| wsrep_local_recv_queue | 0 |
|
| wsrep_local_recv_queue_max | 1 |
|
| wsrep_local_recv_queue_min | 0 |
|
| wsrep_local_recv_queue_avg | 0 |
|
| wsrep_local_cached_downto | 7143 |
|
| wsrep_flow_control_paused_ns | 0 |
|
| wsrep_flow_control_paused | 0 |
|
| wsrep_flow_control_sent | 0 |
|
| wsrep_flow_control_recv | 0 |
|
| wsrep_flow_control_active | false |
|
| wsrep_flow_control_requested | false |
|
| wsrep_cert_deps_distance | 1.21053 |
|
| wsrep_apply_oooe | 0 |
|
| wsrep_apply_oool | 0 |
|
| wsrep_apply_window | 1 |
|
| wsrep_apply_waits | 0 |
|
| wsrep_commit_oooe | 0 |
|
| wsrep_commit_oool | 0 |
|
| wsrep_commit_window | 1 |
|
| wsrep_local_state | 4 |
|
| wsrep_local_state_comment | Synced |
|
| wsrep_cert_index_size | 3785 |
|
| wsrep_causal_reads | 0 |
|
| wsrep_cert_interval | 4323.37 |
|
| wsrep_open_transactions | 0 |
|
| wsrep_open_connections | 0 |
|
| wsrep_incoming_addresses | 10.42.4.127:0,10.42.17.60:0,10.42.6.39:0 |
|
| wsrep_cluster_weight | 3 |
|
| wsrep_desync_count | 0 |
|
| wsrep_evs_delayed | |
|
| wsrep_evs_evict_list | |
|
| wsrep_evs_repl_latency | 0/0/0/0/0 |
|
| wsrep_evs_state | OPERATIONAL |
|
| wsrep_gcomm_uuid | 2993d30e-afff-11ee-89f7-e7f3cd26fa41 |
|
| wsrep_gmcast_segment | 0 |
|
| wsrep_applier_thread_count | 4 |
|
| wsrep_cluster_capabilities | |
|
| wsrep_cluster_conf_id | 33 |
|
| wsrep_cluster_size | 3 |
|
| wsrep_cluster_state_uuid | a11a7c71-9843-11ee-bf01-3e8006b3a5a5 |
|
| wsrep_cluster_status | Primary |
|
| wsrep_connected | ON |
|
| wsrep_local_bf_aborts | 0 |
|
| wsrep_local_index | 0 |
|
| wsrep_provider_capabilities | :MULTI_MASTER:CERTIFICATION:PARALLEL_APPLYING:TRX_REPLAY:ISOLATION:PAUSE:CAUSAL_READS:INCREMENTAL_WRITESET:UNORDERED:PREORDERED:STREAMING:NBO: |
|
| wsrep_provider_name | Galera |
|
| wsrep_provider_vendor | Codership Oy <info@codership.com> |
|
| wsrep_provider_version | 4.13(r0f7af31) |
|
| wsrep_ready | ON |
|
| wsrep_rollbacker_thread_count | 1 |
|
| wsrep_thread_count | 5 |
|
+-------------------------------+------------------------------------------------------------------------------------------------------------------------------------------------+
|
69 rows in set (0.002 sec)
|
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