Mariadb-docker: unable to start new container - InnoDB: Corrupted page

Created on 18 Jul 2020  ·  16Comments  ·  Source: MariaDB/mariadb-docker

After I long pause I resumed the building of a nextcloud instance. When I start the container I get the following error using the same docker-compose file as before. It's a new installation: the database doesn't exist yet.

2020-07-18 21:49:58+02:00 [Note] [Entrypoint]: Entrypoint script for MySQL Server 1:10.5.4+maria~focal started.
2020-07-18 21:49:58+02:00 [Note] [Entrypoint]: Switching to dedicated user 'mysql'
2020-07-18 21:49:58+02:00 [Note] [Entrypoint]: Entrypoint script for MySQL Server 1:10.5.4+maria~focal started.
2020-07-18 21:49:58+02:00 [Note] [Entrypoint]: Initializing database files
2020-07-18 21:49:59 0 [Note] /usr/sbin/mysqld (mysqld 10.5.4-MariaDB-1:10.5.4+maria~focal-log) starting as process 92 ...
2020-07-18 21:49:59 0 [Warning] The parameter innodb_large_prefix is deprecated and has no effect. It may be removed in future releases. See https://mariadb.com/kb/en/library/xtradbinnodb-file-format/
2020-07-18 21:49:59 0 [Note] InnoDB: Using Linux native AIO
2020-07-18 21:49:59 0 [Note] InnoDB: The first innodb_system data file 'ibdata1' did not exist. A new tablespace will be created!
2020-07-18 21:49:59 0 [Note] InnoDB: Uses event mutexes
2020-07-18 21:49:59 0 [Note] InnoDB: Compressed tables use zlib 1.2.11
2020-07-18 21:49:59 0 [Note] InnoDB: Number of pools: 1
2020-07-18 21:49:59 0 [Note] InnoDB: Using ARMv8 crc32 instructions
2020-07-18 21:49:59 0 [Note] mysqld: O_TMPFILE is not supported on /tmp (disabling future attempts)
2020-07-18 21:49:59 0 [Note] InnoDB: Initializing buffer pool, total size = 134217728, chunk size = 134217728
2020-07-18 21:49:59 0 [Note] InnoDB: Completed initialization of buffer pool
2020-07-18 21:49:59 0 [Note] InnoDB: If the mysqld execution user is authorized, page cleaner thread priority can be changed. See the man page of setpriority().
2020-07-18 21:49:59 0 [Note] InnoDB: Setting file './ibdata1' size to 12 MB. Physically writing the file full; Please wait ...
2020-07-18 21:49:59 0 [Note] InnoDB: File './ibdata1' size is now 12 MB.
2020-07-18 21:49:59 0 [Note] InnoDB: Setting log file ./ib_logfile101 size to 100663296 bytes
200718 21:49:59 [ERROR] mysqld got signal 4 ;
This could be because you hit a bug. It is also possible that this binary
or one of the libraries it was linked against is corrupt, improperly built,
or misconfigured. This error can also be caused by malfunctioning hardware.

To report this bug, see https://mariadb.com/kb/en/reporting-bugs

We will try our best to scrape up some info that will hopefully help
diagnose the problem, but since we have already crashed, 
something is definitely wrong and this may fail.

Server version: 10.5.4-MariaDB-1:10.5.4+maria~focal-log
key_buffer_size=134217728
read_buffer_size=131072
max_used_connections=0
max_threads=153
thread_count=0
It is possible that mysqld could use up to 
key_buffer_size + (read_buffer_size + sort_buffer_size)*max_threads = 467809 K  bytes of memory
Hope that's ok; if not, decrease some variables in the equation.

Thread pointer: 0x0
Attempting backtrace. You can use the following information to find out
where mysqld died. If you see no messages after this, something went
terribly wrong...
stack_bottom = 0x0 thread_stack 0x49000
/usr/sbin/mysqld(my_print_stacktrace+0x30)[0x5583740310]
Printing to addr2line failed
/usr/sbin/mysqld(handle_fatal_signal+0x45c)[0x55831eb9bc]
linux-vdso.so.1(__kernel_rt_sigreturn+0x0)[0x7fa0e2d688]
/usr/sbin/mysqld(crc32c_aarch64+0x4b4)[0x5583757adc]
/usr/sbin/mysqld(+0xcf68ec)[0x558361f8ec]
/usr/sbin/mysqld(+0xcf7274)[0x5583620274]
/usr/sbin/mysqld(+0xcf8fa8)[0x5583621fa8]
/usr/sbin/mysqld(+0xcf9f50)[0x5583622f50]
/usr/sbin/mysqld(+0xcfb198)[0x5583624198]
/usr/sbin/mysqld(+0x6090f0)[0x5582f320f0]
/usr/sbin/mysqld(+0xb67cc8)[0x5583490cc8]
/usr/sbin/mysqld(_Z24ha_initialize_handlertonP13st_plugin_int+0x6c)[0x55831ee7f4]
/usr/sbin/mysqld(+0x7057dc)[0x558302e7dc]
/usr/sbin/mysqld(_Z11plugin_initPiPPci+0x864)[0x558302f8b4]
/usr/sbin/mysqld(+0x63f270)[0x5582f68270]
/usr/sbin/mysqld(_Z11mysqld_mainiPPc+0x40c)[0x5582f6dadc]
/lib/aarch64-linux-gnu/libc.so.6(__libc_start_main+0xe8)[0x7fa04bb090]
/usr/sbin/mysqld(+0x639d90)[0x5582f62d90]

My docker-compose:

version: "3.2"

services:
    db:
        image: mariadb

        container_name: nextcloud-db

        command: --transaction-isolation=READ-COMMITTED --log-bin=mysqld-bin --binlog-format=ROW --innodb-file-per-table=ON --innodb-large-prefix=ON --character-set-server=utf8mb4 --collation-server=utf8mb4_general_ci --verbose

        environment:
            - PUID=1000
            - PGID=1000 
            - TZ=Europe/Paris
            - MYSQL_DATABASE_FILE=/run/secrets/nextcloud_db_name
            - MYSQL_USER_FILE=/run/secrets/nextcloud_db_user_name
            - MYSQL_PASSWORD_FILE=/run/secrets/nextcloud_db_user_password
            - MYSQL_ROOT_PASSWORD_FILE=/run/secrets/nextcloud_db_root_password

        volumes:
            - db:/var/lib/mysql

        networks: 
            - default

        expose:
            - "3306"

        restart: unless-stopped

        secrets:
            - nextcloud_db_name
            - nextcloud_db_user_name
            - nextcloud_db_user_password
            - nextcloud_db_root_password

docker version

$ docker version
Client:
 Version:           19.03.12-ce
 API version:       1.40
 Go version:        go1.14.4
 Git commit:        48a66213fe
 Built:             Wed Jul  1 20:52:21 2020
 OS/Arch:           linux/arm64
 Experimental:      false

Server:
 Engine:
  Version:          19.03.12-ce
  API version:      1.40 (minimum version 1.12)
  Go version:       go1.14.4
  Git commit:       48a66213fe
  Built:            Wed Jul  1 20:51:45 2020
  OS/Arch:          linux/arm64
  Experimental:     false
 containerd:
  Version:          v1.3.4.m
  GitCommit:        d76c121f76a5fc8a462dc64594aea72fe18e1178.m
 runc:
  Version:          1.0.0-rc91
  GitCommit:        24a3cf88a7ae5f4995f6750654c0e2ca61ef4bb2
 docker-init:
  Version:          0.18.0
  GitCommit:        fec3683
picture MorgothSauron

Most helpful comment

I just checked 10.5.5 which includes the fix for ARM CPUs having crc32 but missing pmull, and it works again like a charm.

Thanks for fixing this one!

picture alexandresoro on 11 Aug 2020
😄2 🚀1 🎉1

All 16 comments

I'm not able to reproduce on amd64

$ docker-compose up -d
Creating network "root_default" with the default driver
Creating volume "root_db" with default driver
Creating nextcloud-db ... done


docker logs 

$ docker-compose logs
Attaching to nextcloud-db
nextcloud-db | 2020-07-20 19:56:00+02:00 [Note] [Entrypoint]: Entrypoint script for MySQL Server 1:10.5.4+maria~focal started.
nextcloud-db | 2020-07-20 19:56:01+02:00 [Note] [Entrypoint]: Switching to dedicated user 'mysql'
nextcloud-db | 2020-07-20 19:56:01+02:00 [Note] [Entrypoint]: Entrypoint script for MySQL Server 1:10.5.4+maria~focal started.
nextcloud-db | 2020-07-20 19:56:01+02:00 [Note] [Entrypoint]: Initializing database files
nextcloud-db | 2020-07-20 19:56:01 0 [Note] /usr/sbin/mysqld (mysqld 10.5.4-MariaDB-1:10.5.4+maria~focal-log) starting as process 90 ...
nextcloud-db | 2020-07-20 19:56:01 0 [Warning] The parameter innodb_large_prefix is deprecated and has no effect. It may be removed in future releases. See https://mariadb.com/kb/en/library/xtradbinnodb-file-format/
nextcloud-db | 2020-07-20 19:56:01 0 [Note] InnoDB: Using Linux native AIO
nextcloud-db | 2020-07-20 19:56:01 0 [Note] InnoDB: The first innodb_system data file 'ibdata1' did not exist. A new tablespace will be created!
nextcloud-db | 2020-07-20 19:56:01 0 [Note] InnoDB: Uses event mutexes
nextcloud-db | 2020-07-20 19:56:01 0 [Note] InnoDB: Compressed tables use zlib 1.2.11
nextcloud-db | 2020-07-20 19:56:01 0 [Note] InnoDB: Number of pools: 1
nextcloud-db | 2020-07-20 19:56:01 0 [Note] InnoDB: Using SSE4.2 crc32 instructions
nextcloud-db | 2020-07-20 19:56:01 0 [Note] mysqld: O_TMPFILE is not supported on /tmp (disabling future attempts)
nextcloud-db | 2020-07-20 19:56:01 0 [Note] InnoDB: Initializing buffer pool, total size = 134217728, chunk size = 134217728
nextcloud-db | 2020-07-20 19:56:01 0 [Note] InnoDB: Completed initialization of buffer pool
nextcloud-db | 2020-07-20 19:56:01 0 [Note] InnoDB: If the mysqld execution user is authorized, page cleaner thread priority can be changed. See the man page of setpriority().
nextcloud-db | 2020-07-20 19:56:01 0 [Note] InnoDB: Setting file './ibdata1' size to 12 MB. Physically writing the file full; Please wait ...
nextcloud-db | 2020-07-20 19:56:01 0 [Note] InnoDB: File './ibdata1' size is now 12 MB.
nextcloud-db | 2020-07-20 19:56:01 0 [Note] InnoDB: Setting log file ./ib_logfile101 size to 100663296 bytes
nextcloud-db | 2020-07-20 19:56:02 0 [Note] InnoDB: Renaming log file ./ib_logfile101 to ./ib_logfile0
nextcloud-db | 2020-07-20 19:56:02 0 [Note] InnoDB: New log file created, LSN=10312
nextcloud-db | 2020-07-20 19:56:02 0 [Note] InnoDB: Doublewrite buffer not found: creating new
nextcloud-db | 2020-07-20 19:56:02 0 [Note] InnoDB: Doublewrite buffer created
nextcloud-db | 2020-07-20 19:56:02 0 [Note] InnoDB: 128 rollback segments are active.
nextcloud-db | 2020-07-20 19:56:02 0 [Note] InnoDB: Creating foreign key constraint system tables.
nextcloud-db | 2020-07-20 19:56:02 0 [Note] InnoDB: Creating tablespace and datafile system tables.
nextcloud-db | 2020-07-20 19:56:02 0 [Note] InnoDB: Creating sys_virtual system tables.
nextcloud-db | 2020-07-20 19:56:02 0 [Note] InnoDB: Creating shared tablespace for temporary tables
nextcloud-db | 2020-07-20 19:56:02 0 [Note] InnoDB: Setting file './ibtmp1' size to 12 MB. Physically writing the file full; Please wait ...
nextcloud-db | 2020-07-20 19:56:02 0 [Note] InnoDB: File './ibtmp1' size is now 12 MB.
nextcloud-db | 2020-07-20 19:56:02 0 [Note] InnoDB: 10.5.4 started; log sequence number 0; transaction id 7
nextcloud-db | 2020-07-20 19:56:02 1 [Warning] Failed to load slave replication state from table mysql.gtid_slave_pos: 1017: Can't find file: './mysql/' (errno: 2 "No such file or directory")
nextcloud-db | 
nextcloud-db | 
nextcloud-db | PLEASE REMEMBER TO SET A PASSWORD FOR THE MariaDB root USER !
nextcloud-db | To do so, start the server, then issue the following commands:
nextcloud-db | 
nextcloud-db | '/usr/bin/mysqladmin' -u root password 'new-password'
nextcloud-db | '/usr/bin/mysqladmin' -u root -h  password 'new-password'
nextcloud-db | 
nextcloud-db | Alternatively you can run:
nextcloud-db | '/usr/bin/mysql_secure_installation'
nextcloud-db | 
nextcloud-db | which will also give you the option of removing the test
nextcloud-db | databases and anonymous user created by default.  This is
nextcloud-db | strongly recommended for production servers.
nextcloud-db | 
nextcloud-db | See the MariaDB Knowledgebase at https://mariadb.com/kb or the
nextcloud-db | MySQL manual for more instructions.
nextcloud-db | 
nextcloud-db | Please report any problems at https://mariadb.org/jira
nextcloud-db | 
nextcloud-db | The latest information about MariaDB is available at https://mariadb.org/.
nextcloud-db | You can find additional information about the MySQL part at:
nextcloud-db | https://dev.mysql.com
nextcloud-db | Consider joining MariaDB's strong and vibrant community:
nextcloud-db | https://mariadb.org/get-involved/
nextcloud-db | 
nextcloud-db | 2020-07-20 19:56:03+02:00 [Note] [Entrypoint]: Database files initialized
nextcloud-db | 2020-07-20 19:56:03+02:00 [Note] [Entrypoint]: Starting temporary server
nextcloud-db | 2020-07-20 19:56:03+02:00 [Note] [Entrypoint]: Waiting for server startup
nextcloud-db | 2020-07-20 19:56:03 0 [Note] mysqld (mysqld 10.5.4-MariaDB-1:10.5.4+maria~focal-log) starting as process 117 ...
nextcloud-db | 2020-07-20 19:56:03 0 [Warning] The parameter innodb_large_prefix is deprecated and has no effect. It may be removed in future releases. See https://mariadb.com/kb/en/library/xtradbinnodb-file-format/
nextcloud-db | 2020-07-20 19:56:03 0 [Note] InnoDB: Using Linux native AIO
nextcloud-db | 2020-07-20 19:56:03 0 [Note] InnoDB: Uses event mutexes
nextcloud-db | 2020-07-20 19:56:03 0 [Note] InnoDB: Compressed tables use zlib 1.2.11
nextcloud-db | 2020-07-20 19:56:03 0 [Note] InnoDB: Number of pools: 1
nextcloud-db | 2020-07-20 19:56:03 0 [Note] InnoDB: Using SSE4.2 crc32 instructions
nextcloud-db | 2020-07-20 19:56:03 0 [Note] mysqld: O_TMPFILE is not supported on /tmp (disabling future attempts)
nextcloud-db | 2020-07-20 19:56:03 0 [Note] InnoDB: Initializing buffer pool, total size = 134217728, chunk size = 134217728
nextcloud-db | 2020-07-20 19:56:03 0 [Note] InnoDB: Completed initialization of buffer pool
nextcloud-db | 2020-07-20 19:56:03 0 [Note] InnoDB: If the mysqld execution user is authorized, page cleaner thread priority can be changed. See the man page of setpriority().
nextcloud-db | 2020-07-20 19:56:03 0 [Note] InnoDB: 128 rollback segments are active.
nextcloud-db | 2020-07-20 19:56:03 0 [Note] InnoDB: Creating shared tablespace for temporary tables
nextcloud-db | 2020-07-20 19:56:03 0 [Note] InnoDB: Setting file './ibtmp1' size to 12 MB. Physically writing the file full; Please wait ...
nextcloud-db | 2020-07-20 19:56:03 0 [Note] InnoDB: File './ibtmp1' size is now 12 MB.
nextcloud-db | 2020-07-20 19:56:03 0 [Note] InnoDB: 10.5.4 started; log sequence number 45041; transaction id 21
nextcloud-db | 2020-07-20 19:56:03 0 [Note] Plugin 'FEEDBACK' is disabled.
nextcloud-db | 2020-07-20 19:56:03 0 [Note] InnoDB: Loading buffer pool(s) from /var/lib/mysql/ib_buffer_pool
nextcloud-db | 2020-07-20 19:56:03 0 [Note] InnoDB: Buffer pool(s) load completed at 200720 19:56:03
nextcloud-db | 2020-07-20 19:56:03 0 [Warning] 'user' entry 'root@89424b1f6855' ignored in --skip-name-resolve mode.
nextcloud-db | 2020-07-20 19:56:03 0 [Warning] 'user' entry '@89424b1f6855' ignored in --skip-name-resolve mode.
nextcloud-db | 2020-07-20 19:56:03 0 [Warning] 'proxies_priv' entry '@% root@89424b1f6855' ignored in --skip-name-resolve mode.
nextcloud-db | 2020-07-20 19:56:03 0 [Note] Reading of all Master_info entries succeeded
nextcloud-db | 2020-07-20 19:56:03 0 [Note] Added new Master_info '' to hash table
nextcloud-db | 2020-07-20 19:56:03 0 [Note] mysqld: ready for connections.
nextcloud-db | Version: '10.5.4-MariaDB-1:10.5.4+maria~focal-log'  socket: '/run/mysqld/mysqld.sock'  port: 0  mariadb.org binary distribution
nextcloud-db | 2020-07-20 19:56:04+02:00 [Note] [Entrypoint]: Temporary server started.
nextcloud-db | Warning: Unable to load '/usr/share/zoneinfo/leap-seconds.list' as time zone. Skipping it.
nextcloud-db | Warning: Unable to load '/usr/share/zoneinfo/leapseconds' as time zone. Skipping it.
nextcloud-db | Warning: Unable to load '/usr/share/zoneinfo/tzdata.zi' as time zone. Skipping it.
nextcloud-db | 2020-07-20 19:56:11 6 [Warning] 'proxies_priv' entry '@% root@89424b1f6855' ignored in --skip-name-resolve mode.
nextcloud-db | 2020-07-20 19:56:11+02:00 [Note] [Entrypoint]: Creating user nextcloud_db_user_name
nextcloud-db | 2020-07-20 19:56:11 8 [Warning] 'proxies_priv' entry '@% root@89424b1f6855' ignored in --skip-name-resolve mode.
nextcloud-db | 
nextcloud-db | 2020-07-20 19:56:11+02:00 [Note] [Entrypoint]: Stopping temporary server
nextcloud-db | 2020-07-20 19:56:11 0 [Note] mysqld (initiated by: root[root] @ localhost []): Normal shutdown
nextcloud-db | 2020-07-20 19:56:11 0 [Note] Event Scheduler: Purging the queue. 0 events
nextcloud-db | 2020-07-20 19:56:11 0 [Note] InnoDB: FTS optimize thread exiting.
nextcloud-db | 2020-07-20 19:56:11 0 [Note] InnoDB: Starting shutdown...
nextcloud-db | 2020-07-20 19:56:11 0 [Note] InnoDB: Dumping buffer pool(s) to /var/lib/mysql/ib_buffer_pool
nextcloud-db | 2020-07-20 19:56:11 0 [Note] InnoDB: Buffer pool(s) dump completed at 200720 19:56:11
nextcloud-db | 2020-07-20 19:56:13 0 [Note] InnoDB: Shutdown completed; log sequence number 45081; transaction id 24
nextcloud-db | 2020-07-20 19:56:13 0 [Note] InnoDB: Removed temporary tablespace data file: "ibtmp1"
nextcloud-db | 2020-07-20 19:56:13 0 [Note] mysqld: Shutdown complete
nextcloud-db | 
nextcloud-db | 2020-07-20 19:56:13+02:00 [Note] [Entrypoint]: Temporary server stopped
nextcloud-db | 
nextcloud-db | 2020-07-20 19:56:13+02:00 [Note] [Entrypoint]: MySQL init process done. Ready for start up.
nextcloud-db | 
nextcloud-db | 2020-07-20 19:56:14 0 [Note] mysqld (mysqld 10.5.4-MariaDB-1:10.5.4+maria~focal-log) starting as process 1 ...
nextcloud-db | 2020-07-20 19:56:14 0 [Warning] The parameter innodb_large_prefix is deprecated and has no effect. It may be removed in future releases. See https://mariadb.com/kb/en/library/xtradbinnodb-file-format/
nextcloud-db | 2020-07-20 19:56:14 0 [Note] InnoDB: Using Linux native AIO
nextcloud-db | 2020-07-20 19:56:14 0 [Note] InnoDB: Uses event mutexes
nextcloud-db | 2020-07-20 19:56:14 0 [Note] InnoDB: Compressed tables use zlib 1.2.11
nextcloud-db | 2020-07-20 19:56:14 0 [Note] InnoDB: Number of pools: 1
nextcloud-db | 2020-07-20 19:56:14 0 [Note] InnoDB: Using SSE4.2 crc32 instructions
nextcloud-db | 2020-07-20 19:56:14 0 [Note] mysqld: O_TMPFILE is not supported on /tmp (disabling future attempts)
nextcloud-db | 2020-07-20 19:56:14 0 [Note] InnoDB: Initializing buffer pool, total size = 134217728, chunk size = 134217728
nextcloud-db | 2020-07-20 19:56:14 0 [Note] InnoDB: Completed initialization of buffer pool
nextcloud-db | 2020-07-20 19:56:14 0 [Note] InnoDB: If the mysqld execution user is authorized, page cleaner thread priority can be changed. See the man page of setpriority().
nextcloud-db | 2020-07-20 19:56:14 0 [Note] InnoDB: 128 rollback segments are active.
nextcloud-db | 2020-07-20 19:56:14 0 [Note] InnoDB: Creating shared tablespace for temporary tables
nextcloud-db | 2020-07-20 19:56:14 0 [Note] InnoDB: Setting file './ibtmp1' size to 12 MB. Physically writing the file full; Please wait ...
nextcloud-db | 2020-07-20 19:56:14 0 [Note] InnoDB: File './ibtmp1' size is now 12 MB.
nextcloud-db | 2020-07-20 19:56:14 0 [Note] InnoDB: 10.5.4 started; log sequence number 45081; transaction id 21
nextcloud-db | 2020-07-20 19:56:14 0 [Note] Plugin 'FEEDBACK' is disabled.
nextcloud-db | 2020-07-20 19:56:14 0 [Note] InnoDB: Loading buffer pool(s) from /var/lib/mysql/ib_buffer_pool
nextcloud-db | 2020-07-20 19:56:14 0 [Note] InnoDB: Buffer pool(s) load completed at 200720 19:56:14
nextcloud-db | 2020-07-20 19:56:14 0 [Note] Server socket created on IP: '::'.
nextcloud-db | 2020-07-20 19:56:14 0 [Warning] 'proxies_priv' entry '@% root@89424b1f6855' ignored in --skip-name-resolve mode.
nextcloud-db | 2020-07-20 19:56:14 0 [Note] Reading of all Master_info entries succeeded
nextcloud-db | 2020-07-20 19:56:14 0 [Note] Added new Master_info '' to hash table
nextcloud-db | 2020-07-20 19:56:14 0 [Note] mysqld: ready for connections.
nextcloud-db | Version: '10.5.4-MariaDB-1:10.5.4+maria~focal-log'  socket: '/run/mysqld/mysqld.sock'  port: 3306  mariadb.org binary distribution

[ERROR] mysqld got signal 4

How are the resources on your system? Especially considering it's an arm64 device is the memory getting maxed out triggering an OOMkill?

wglambert picture wglambert on 20 Jul 2020

I don't see any message in dmesg that would indicate that OOMkill happens.

This is a Pi4 with 4Gb of RAM. Right now it's only running a PiHole and Unbound, each using less than 1% of memory. There is nothing else running.

MorgothSauron picture MorgothSauron on 20 Jul 2020

Hello,

I got the very same issue, also with a Pi 4 4GB. So it may be an issue that only occurs on arm64 ?

I noticed is that it occurred when migrating from 10.4 to 10.5 on an existing database, but also with a fresh database.

I managed to reproduce with 10.5.1 but the issue cannot be reproduced on latest 10.4 (10.4.13 I believe).

Edit:

I ran the basic command:

sudo docker run -e MYSQL_RANDOM_ROOT_PASSWORD=true mariadb

Please find the dump below,

stdout:

``` 2020-07-20 22:01:03+00:00 [Note] [Entrypoint]: Entrypoint script for MySQL Server 1:10.5.4+maria~focal started.
2020-07-20 22:01:03+00:00 [Note] [Entrypoint]: Switching to dedicated user 'mysql'
2020-07-20 22:01:03+00:00 [Note] [Entrypoint]: Entrypoint script for MySQL Server 1:10.5.4+maria~focal started.
2020-07-20 22:01:03+00:00 [Note] [Entrypoint]: Initializing database files

Installation of system tables failed! Examine the logs in
/var/lib/mysql/ for more information.

The problem could be conflicting information in an external
my.cnf files. You can ignore these by doing:

shell> /usr/bin/mysql_install_db --defaults-file=~/.my.cnf

You can also try to start the mysqld daemon with:

shell> /usr/sbin/mysqld --skip-grant-tables --general-log &

and use the command line tool /usr/bin/mysql
to connect to the mysql database and look at the grant tables:

shell> /usr/bin/mysql -u root mysql
mysql> show tables;

Try 'mysqld --help' if you have problems with paths. Using
--general-log gives you a log in /var/lib/mysql/ that may be helpful.

The latest information about mysql_install_db is available at
https://mariadb.com/kb/en/installing-system-tables-mysql_install_db
You can find the latest source at https://downloads.mariadb.org and
the maria-discuss email list at https://launchpad.net/~maria-discuss

Please check all of the above before submitting a bug report
at https://mariadb.org/jira

`stderr`:

``` 200720 22:01:03 [ERROR] mysqld got signal 4 ;
This could be because you hit a bug. It is also possible that this binary
or one of the libraries it was linked against is corrupt, improperly built,
or misconfigured. This error can also be caused by malfunctioning hardware.

To report this bug, see https://mariadb.com/kb/en/reporting-bugs

We will try our best to scrape up some info that will hopefully help
diagnose the problem, but since we have already crashed, 
something is definitely wrong and this may fail.

Server version: 10.5.4-MariaDB-1:10.5.4+maria~focal
key_buffer_size=134217728
read_buffer_size=131072
max_used_connections=0
max_threads=153
thread_count=0
It is possible that mysqld could use up to 
key_buffer_size + (read_buffer_size + sort_buffer_size)*max_threads = 467809 K  bytes of memory
Hope that's ok; if not, decrease some variables in the equation.

Thread pointer: 0x0
Attempting backtrace. You can use the following information to find out
where mysqld died. If you see no messages after this, something went
terribly wrong...
stack_bottom = 0x0 thread_stack 0x49000
/usr/sbin/mysqld(my_print_stacktrace+0x30)[0xaaaad1e0b310]
Printing to addr2line failed
/usr/sbin/mysqld(handle_fatal_signal+0x45c)[0xaaaad18b69bc]
linux-vdso.so.1(__kernel_rt_sigreturn+0x0)[0xffffa2d915b0]
/usr/sbin/mysqld(crc32c_aarch64+0x4b4)[0xaaaad1e22adc]
/usr/sbin/mysqld(+0xcf68ec)[0xaaaad1cea8ec]
/usr/sbin/mysqld(+0xcf7274)[0xaaaad1ceb274]
/usr/sbin/mysqld(+0xcf8fa8)[0xaaaad1cecfa8]
/usr/sbin/mysqld(+0xcf9f50)[0xaaaad1cedf50]
/usr/sbin/mysqld(+0xcfb198)[0xaaaad1cef198]
/usr/sbin/mysqld(+0x6090f0)[0xaaaad15fd0f0]
/usr/sbin/mysqld(+0xb67cc8)[0xaaaad1b5bcc8]
/usr/sbin/mysqld(_Z24ha_initialize_handlertonP13st_plugin_int+0x6c)[0xaaaad18b97f4]
/usr/sbin/mysqld(+0x7057dc)[0xaaaad16f97dc]
/usr/sbin/mysqld(_Z11plugin_initPiPPci+0x864)[0xaaaad16fa8b4]
/usr/sbin/mysqld(+0x63f270)[0xaaaad1633270]
/usr/sbin/mysqld(_Z11mysqld_mainiPPc+0x40c)[0xaaaad1638adc]
/lib/aarch64-linux-gnu/libc.so.6(__libc_start_main+0xe8)[0xffffa241f090]
/usr/sbin/mysqld(+0x639d90)[0xaaaad162dd90]
The manual page at http://dev.mysql.com/doc/mysql/en/crashing.html contains
information that should help you find out what is causing the crash.
Writing a core file...
Working directory at /var/lib/mysql
Resource Limits:
Limit                     Soft Limit           Hard Limit           Units     
Max cpu time              unlimited            unlimited            seconds   
Max file size             unlimited            unlimited            bytes     
Max data size             unlimited            unlimited            bytes     
Max stack size            8388608              unlimited            bytes     
Max core file size        unlimited            unlimited            bytes     
Max resident set          unlimited            unlimited            bytes     
Max processes             unlimited            unlimited            processes 
Max open files            1048576              1048576              files     
Max locked memory         65536                65536                bytes     
Max address space         unlimited            unlimited            bytes     
Max file locks            unlimited            unlimited            locks     
Max pending signals       14780                14780                signals   
Max msgqueue size         819200               819200               bytes     
Max nice priority         0                    0                    
Max realtime priority     0                    0                    
Max realtime timeout      unlimited            unlimited            us        
Core pattern: |/usr/share/apport/apport %p %s %c %d %P %E

Illegal instruction (core dumped)
alexandresoro picture alexandresoro on 20 Jul 2020

I tried version 10.4.13 with the same docker-compose file on the same pi4 and it is working.

nextcloud-db | 2020-07-21 18:42:38+02:00 [Note] [Entrypoint]: Database files initialized
nextcloud-db | 2020-07-21 18:42:38+02:00 [Note] [Entrypoint]: Starting temporary server
nextcloud-db | 2020-07-21 18:42:38+02:00 [Note] [Entrypoint]: Waiting for server startup
nextcloud-db | 2020-07-21 18:42:38 0 [Note] mysqld (mysqld 10.4.13-MariaDB-1:10.4.13+maria~focal-log) starting as process 124 ...
nextcloud-db | 2020-07-21 18:42:38 0 [Warning] The parameter innodb_large_prefix is deprecated and has no effect. It may be removed in future releases. See https://mariadb.com/kb/en/library/xtradbinnodb-file-format/
nextcloud-db | 2020-07-21 18:42:38 0 [Note] InnoDB: Using Linux native AIO
nextcloud-db | 2020-07-21 18:42:38 0 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
nextcloud-db | 2020-07-21 18:42:38 0 [Note] InnoDB: Uses event mutexes
nextcloud-db | 2020-07-21 18:42:38 0 [Note] InnoDB: Compressed tables use zlib 1.2.11
nextcloud-db | 2020-07-21 18:42:38 0 [Note] InnoDB: Number of pools: 1
nextcloud-db | 2020-07-21 18:42:38 0 [Note] InnoDB: Using generic crc32 instructions
nextcloud-db | 2020-07-21 18:42:38 0 [Note] mysqld: O_TMPFILE is not supported on /tmp (disabling future attempts)
nextcloud-db | 2020-07-21 18:42:38 0 [Note] InnoDB: Initializing buffer pool, total size = 256M, instances = 1, chunk size = 128M
nextcloud-db | 2020-07-21 18:42:38 0 [Note] InnoDB: Completed initialization of buffer pool
nextcloud-db | 2020-07-21 18:42:38 0 [Note] InnoDB: If the mysqld execution user is authorized, page cleaner thread priority can be changed. See the man page of setpriority().
nextcloud-db | 2020-07-21 18:42:38 0 [Note] InnoDB: 128 out of 128 rollback segments are active.
nextcloud-db | 2020-07-21 18:42:38 0 [Note] InnoDB: Creating shared tablespace for temporary tables
nextcloud-db | 2020-07-21 18:42:38 0 [Note] InnoDB: Setting file './ibtmp1' size to 12 MB. Physically writing the file full; Please wait ...
nextcloud-db | 2020-07-21 18:42:38 0 [Note] InnoDB: File './ibtmp1' size is now 12 MB.
nextcloud-db | 2020-07-21 18:42:38 0 [Note] InnoDB: Waiting for purge to start
nextcloud-db | 2020-07-21 18:42:38 0 [Note] InnoDB: 10.4.13 started; log sequence number 60972; transaction id 21
nextcloud-db | 2020-07-21 18:42:38 0 [Note] InnoDB: Loading buffer pool(s) from /var/lib/mysql/ib_buffer_pool
nextcloud-db | 2020-07-21 18:42:38 0 [Note] Plugin 'FEEDBACK' is disabled.
nextcloud-db | 2020-07-21 18:42:38 0 [Note] InnoDB: Buffer pool(s) load completed at 200721 18:42:38
nextcloud-db | 2020-07-21 18:42:38 0 [Warning] 'user' entry 'root@8ebd26088651' ignored in --skip-name-resolve mode.
nextcloud-db | 2020-07-21 18:42:38 0 [Warning] 'user' entry '@8ebd26088651' ignored in --skip-name-resolve mode.
nextcloud-db | 2020-07-21 18:42:38 0 [Warning] 'proxies_priv' entry '@% root@8ebd26088651' ignored in --skip-name-resolve mode.
nextcloud-db | 2020-07-21 18:42:38 0 [Note] Reading of all Master_info entries succeeded
nextcloud-db | 2020-07-21 18:42:38 0 [Note] Added new Master_info '' to hash table
nextcloud-db | 2020-07-21 18:42:38 0 [Note] mysqld: ready for connections.
nextcloud-db | Version: '10.4.13-MariaDB-1:10.4.13+maria~focal-log'  socket: '/var/run/mysqld/mysqld.sock'  port: 0  mariadb.org binary distribution
nextcloud-db | 2020-07-21 18:42:39+02:00 [Note] [Entrypoint]: Temporary server started.
MorgothSauron picture MorgothSauron on 21 Jul 2020

Hello,

I have also an error message because of anything with InnoDB:

[ERROR] InnoDB: Corrupted page [page id: space=0, page number=0] of datafile './ibdata1' could not be found in the doublewrite buffer.

_My System:_ Odroid C2 (arm64), Debian Buster.

_Parts of my docker-compose.yml_:

>
>

version: "3"
services:
[..]
db:
container_name: mariadb
image: arm64v8/mariadb:latest
restart: always
environment:
MYSQL_ROOT_PASSWORD: "**"
MYSQL_DATABASE: "**"
MYSQL_USER: "**"
MYSQL_PASSWORD: "**"
volumes:
- ./data/mysql:/var/lib/mysql
- /etc/localtime:/etc/localtime:ro
networks:
nginx-proxy-manager_default:
ipv4_address: 172.224.1.255
[..]
volumes:
[..]
db:

networks:
nginx-proxy-manager_default:
ipam:
driver: default
config:
- subnet: 172.224.0.0/16

_My error-log (from 'docker logs mariadb'):_

>
>

2020-07-24 20:50:00+02:00 [Note] [Entrypoint]: Entrypoint script for MySQL Server 1:10.5.4+maria~focal started.
2020-07-24 20:50:01+02:00 [Note] [Entrypoint]: Switching to dedicated user 'mysql'
2020-07-24 20:50:01+02:00 [Note] [Entrypoint]: Entrypoint script for MySQL Server 1:10.5.4+maria~focal started.
2020-07-24 20:50:01+02:00 [Note] [Entrypoint]: Initializing database files
2020-07-24 20:50:01 0 [ERROR] InnoDB: Corrupted page [page id: space=0, page number=0] of datafile './ibdata1' could not be found in the doublewrite buffer.
2020-07-24 20:50:01 0 [ERROR] InnoDB: Plugin initialization aborted with error Data structure corruption
2020-07-24 20:50:02 0 [ERROR] Plugin 'InnoDB' init function returned error.
2020-07-24 20:50:02 0 [ERROR] Plugin 'InnoDB' registration as a STORAGE ENGINE failed.
2020-07-24 20:50:02 0 [ERROR] Unknown/unsupported storage engine: InnoDB
2020-07-24 20:50:02 0 [ERROR] Aborting

Installation of system tables failed! Examine the logs in
/var/lib/mysql/ for more information.

The problem could be conflicting information in an external
my.cnf files. You can ignore these by doing:

shell> /usr/bin/mysql_install_db --defaults-file=~/.my.cnf

You can also try to start the mysqld daemon with:

shell> /usr/sbin/mysqld --skip-grant-tables --general-log &

and use the command line tool /usr/bin/mysql
to connect to the mysql database and look at the grant tables:

shell> /usr/bin/mysql -u root mysql
mysql> show tables;

Try 'mysqld --help' if you have problems with paths. Using
--general-log gives you a log in /var/lib/mysql/ that may be helpful.

The latest information about mysql_install_db is available at
https://mariadb.com/kb/en/installing-system-tables-mysql_install_db
You can find the latest source at https://downloads.mariadb.org and
the maria-discuss email list at https://launchpad.net/~maria-discuss

Please check all of the above before submitting a bug report
at https://mariadb.org/jira

May someone know a solution for this?

Mathias

wahoonie76 picture wahoonie76 on 24 Jul 2020

definitely broke on arm64. going down to 10.4.x or lower solves all issues

awill1988 picture awill1988 on 27 Jul 2020

It looks like this problem was originally introduced by MariaDB/server@0928596a8bd54c3ec85462eb4993464eac19f8f2 in MariaDB 10.5.0. We are probably missing some run-time check.

dr-m picture dr-m on 29 Jul 2020
❤2 👀1

@MorgothSauron
Can you run following code snippet and share the output

include

using namespace std;

include

include

int main() {
cout << "is CRC32 support (HWCAP_CRC32) "
<< ((getauxval(AT_HWCAP) & HWCAP_CRC32) ? "true" : "false") << endl;
cout << "is PMULL support (HWCAP_PMULL) "
<< ((getauxval(AT_HWCAP) & HWCAP_PMULL) ? "true" : "false") << endl;
}

mysqlonarm picture mysqlonarm on 29 Jul 2020

Hi @mysqlonarm ,

I tested your script on my platform which is exactly the same as @MorgothSauron .
Please find the output below:

is CRC32 support (HWCAP_CRC32) true
is PMULL support (HWCAP_PMULL) false

Hope it helps

alexandresoro picture alexandresoro on 29 Jul 2020
👍1

Thanks @alexandresoro. That explains. So we will have to add runtime check for said instruction too.

mysqlonarm picture mysqlonarm on 29 Jul 2020

@alexandresoro Can you also share the output of lscpu. What I am wondering is PI4 has cortex a-72 processor that should technically has pmull support so wanted to re-validate what lscpu report.

mysqlonarm picture mysqlonarm on 29 Jul 2020

Sure, please find it below:

❯ lscpu alex@pi  0.14  13%  2.78G  17:40:34
Architecture: aarch64
CPU op-mode(s): 32-bit, 64-bit
Byte Order: Little Endian
CPU(s): 4
On-line CPU(s) list: 0-3
Thread(s) per core: 1
Core(s) per socket: 4
Socket(s): 1
Vendor ID: ARM
Model: 3
Model name: Cortex-A72
Stepping: r0p3
CPU max MHz: 1500.0000
CPU min MHz: 600.0000
BogoMIPS: 108.00
Vulnerability Itlb multihit: Not affected
Vulnerability L1tf: Not affected
Vulnerability Mds: Not affected
Vulnerability Meltdown: Not affected
Vulnerability Spec store bypass: Vulnerable
Vulnerability Spectre v1: Mitigation; __user pointer sa
nitization
Vulnerability Spectre v2: Vulnerable
Vulnerability Srbds: Not affected
Vulnerability Tsx async abort: Not affected
Flags: fp asimd evtstrm crc32 cpuid

Let me know if this is enough, I have limited access to it right now, but I could check later on if needed.

alexandresoro picture alexandresoro on 29 Jul 2020
👍1

Thanks @alexandresoro. This should be fine. so the said model is confirmed to have crc32 support w/o pmull support.

mysqlonarm picture mysqlonarm on 29 Jul 2020

This looks to be indeed something that is not mandatory on armv8 architecture if this comment is still valid:

https://github.com/google/crc32c/pull/6#issuecomment-328713398

alexandresoro picture alexandresoro on 29 Jul 2020

I just checked 10.5.5 which includes the fix for ARM CPUs having crc32 but missing pmull, and it works again like a charm.

Thanks for fixing this one!

alexandresoro picture alexandresoro on 11 Aug 2020
😄2 🚀1 🎉1

MDEV-23030 fixed in 10.5.5

grooverdan picture grooverdan on 2 Mar 2021
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