Server crash when trying to alter add Primary Key to InnoDB table

CREATE TABLE `atest` (

  `id` int NOT NULL,

  `name` varchar(20) NOT NULL

) ENGINE=InnoDB;

ALTER TABLE `atest` ADD PRIMARY KEY (`id`);

-- When the container is started

Database initialized

MySQL init process in progress...

2019-02-24 15:51:29 0 [Note] mysqld (mysqld 10.3.13-MariaDB-1:10.3.13+maria~bionic-log) starting as process 109 ...

2019-02-24 15:51:29 0 [Warning] Setting lower_case_table_names=2 because file system for /var/lib/mysql/ is case insensitive

2019-02-24 15:51:29 0 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins

2019-02-24 15:51:29 0 [Note] InnoDB: Uses event mutexes

2019-02-24 15:51:29 0 [Note] InnoDB: Compressed tables use zlib 1.2.11

2019-02-24 15:51:29 0 [Note] InnoDB: Number of pools: 1

2019-02-24 15:51:29 0 [Note] InnoDB: Using SSE2 crc32 instructions

2019-02-24 15:51:29 0 [Note] InnoDB: Initializing buffer pool, total size = 256M, instances = 1, chunk size = 128M

2019-02-24 15:51:29 0 [Note] InnoDB: Completed initialization of buffer pool

2019-02-24 15:51:29 0 [Note] InnoDB: If the mysqld execution user is authorized, page cleaner thread priority can be changed. See the man page of setpriority().

2019-02-24 15:51:30 0 [Note] InnoDB: 128 out of 128 rollback segments are active.

2019-02-24 15:51:30 0 [Note] InnoDB: Creating shared tablespace for temporary tables

2019-02-24 15:51:30 0 [Note] InnoDB: Setting file './ibtmp1' size to 12 MB. Physically writing the file full; Please wait ...

MySQL init process in progress...

2019-02-24 15:51:30 0 [Note] InnoDB: File './ibtmp1' size is now 12 MB.

2019-02-24 15:51:30 0 [Note] InnoDB: Waiting for purge to start

2019-02-24 15:51:31 0 [Note] InnoDB: 10.3.13 started; log sequence number 1630824; transaction id 21

2019-02-24 15:51:31 0 [Note] Plugin 'FEEDBACK' is disabled.

2019-02-24 15:51:31 0 [Note] InnoDB: Loading buffer pool(s) from /var/lib/mysql/ib_buffer_pool

2019-02-24 15:51:31 0 [Note] InnoDB: Buffer pool(s) load completed at 190224 15:51:31

2019-02-24 15:51:31 0 [Warning] 'user' entry 'root@865e711deccc' ignored in --skip-name-resolve mode.

2019-02-24 15:51:31 0 [Warning] 'user' entry '@865e711deccc' ignored in --skip-name-resolve mode.

2019-02-24 15:51:31 0 [Warning] 'proxies_priv' entry '@% root@865e711deccc' ignored in --skip-name-resolve mode.

2019-02-24 15:51:31 0 [Note] Reading of all Master_info entries succeded

2019-02-24 15:51:31 0 [Note] Added new Master_info '' to hash table

2019-02-24 15:51:31 0 [Note] mysqld: ready for connections.

Version: '10.3.13-MariaDB-1:10.3.13+maria~bionic-log'  socket: '/var/run/mysqld/mysqld.sock'  port: 0  mariadb.org binary distribution

Warning: Unable to load '/usr/share/zoneinfo/leap-seconds.list' as time zone. Skipping it.

2019-02-24 15:52:10 11 [Warning] 'proxies_priv' entry '@% root@865e711deccc' ignored in --skip-name-resolve mode.

2019-02-24 15:52:10 0 [Note] mysqld (initiated by: unknown): Normal shutdown

2019-02-24 15:52:10 0 [Note] InnoDB: FTS optimize thread exiting.

2019-02-24 15:52:10 0 [Note] Event Scheduler: Purging the queue. 0 events

2019-02-24 15:52:10 0 [Note] InnoDB: Starting shutdown...

2019-02-24 15:52:10 0 [Note] InnoDB: Dumping buffer pool(s) to /var/lib/mysql/ib_buffer_pool

2019-02-24 15:52:11 0 [Note] InnoDB: Buffer pool(s) dump completed at 190224 15:52:11

2019-02-24 15:52:11 0 [Note] InnoDB: Shutdown completed; log sequence number 1630833; transaction id 24

2019-02-24 15:52:11 0 [Note] InnoDB: Removed temporary tablespace data file: "ibtmp1"

2019-02-24 15:52:11 0 [Note] mysqld: Shutdown complete

MySQL init process done. Ready for start up.

2019-02-24 15:52:11 0 [Note] mysqld (mysqld 10.3.13-MariaDB-1:10.3.13+maria~bionic-log) starting as process 1 ...

2019-02-24 15:52:11 0 [Warning] Setting lower_case_table_names=2 because file system for /var/lib/mysql/ is case insensitive

2019-02-24 15:52:11 0 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins

2019-02-24 15:52:11 0 [Note] InnoDB: Uses event mutexes

2019-02-24 15:52:11 0 [Note] InnoDB: Compressed tables use zlib 1.2.11

2019-02-24 15:52:11 0 [Note] InnoDB: Number of pools: 1

2019-02-24 15:52:11 0 [Note] InnoDB: Using SSE2 crc32 instructions

2019-02-24 15:52:11 0 [Note] InnoDB: Initializing buffer pool, total size = 256M, instances = 1, chunk size = 128M

2019-02-24 15:52:11 0 [Note] InnoDB: Completed initialization of buffer pool

2019-02-24 15:52:11 0 [Note] InnoDB: If the mysqld execution user is authorized, page cleaner thread priority can be changed. See the man page of setpriority().

2019-02-24 15:52:11 0 [Note] InnoDB: 128 out of 128 rollback segments are active.

2019-02-24 15:52:11 0 [Note] InnoDB: Creating shared tablespace for temporary tables

2019-02-24 15:52:11 0 [Note] InnoDB: Setting file './ibtmp1' size to 12 MB. Physically writing the file full; Please wait ...

2019-02-24 15:52:12 0 [Note] InnoDB: File './ibtmp1' size is now 12 MB.

2019-02-24 15:52:12 0 [Note] InnoDB: Waiting for purge to start

2019-02-24 15:52:12 0 [Note] InnoDB: 10.3.13 started; log sequence number 1630833; transaction id 21

2019-02-24 15:52:12 0 [Note] Plugin 'FEEDBACK' is disabled.

2019-02-24 15:52:12 0 [Note] InnoDB: Loading buffer pool(s) from /var/lib/mysql/ib_buffer_pool

2019-02-24 15:52:12 0 [Note] InnoDB: Buffer pool(s) load completed at 190224 15:52:12

2019-02-24 15:52:12 0 [Note] Server socket created on IP: '::'.

2019-02-24 15:52:13 0 [Warning] 'proxies_priv' entry '@% root@865e711deccc' ignored in --skip-name-resolve mode.

2019-02-24 15:52:13 0 [Note] Reading of all Master_info entries succeded

2019-02-24 15:52:13 0 [Note] Added new Master_info '' to hash table

2019-02-24 15:52:13 0 [Note] mysqld: ready for connections.

Version: '10.3.13-MariaDB-1:10.3.13+maria~bionic-log'  socket: '/var/run/mysqld/mysqld.sock'  port: 3306  mariadb.org binary distribution

2019-02-24 15:52:56 9 [ERROR] InnoDB: Operating system error number 26 in a file operation.

2019-02-24 15:52:56 9 [ERROR] InnoDB: Error number 26 means 'Text file busy'

2019-02-24 15:52:56 9 [Note] InnoDB: Some operating system error numbers are described at https://mariadb.com/kb/en/library/operating-system-error-codes/

2019-02-24 15:52:56 9 [ERROR] InnoDB: Cannot rename file './appziodb/atest.ibd' to './appziodb/#sql-ib21.ibd'

2019-02-24 15:52:56 0x7fa05cc58700  InnoDB: Assertion failure in file /home/buildbot/buildbot/build/mariadb-10.3.13/storage/innobase/handler/handler0alter.cc line 8817

InnoDB: Failing assertion: error == DB_SUCCESS

InnoDB: We intentionally generate a memory trap.

InnoDB: Submit a detailed bug report to https://jira.mariadb.org/

InnoDB: If you get repeated assertion failures or crashes, even

InnoDB: immediately after the mysqld startup, there may be

InnoDB: corruption in the InnoDB tablespace. Please refer to

InnoDB: https://mariadb.com/kb/en/library/innodb-recovery-modes/

InnoDB: about forcing recovery.

190224 15:52:56 [ERROR] mysqld got signal 6 ;

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: 10.3.13-MariaDB-1:10.3.13+maria~bionic-log

key_buffer_size=134217728

read_buffer_size=2097152

max_used_connections=1

max_threads=102

thread_count=8

It is possible that mysqld could use up to

key_buffer_size + (read_buffer_size + sort_buffer_size)*max_threads = 760012 K  bytes of memory

Hope that's ok; if not, decrease some variables in the equation.

Thread pointer: 0x7fa02400a498

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 = 0x7fa05cc57dd8 thread_stack 0x49000

mysqld(my_print_stacktrace+0x2e)[0x5560d5ade47e]

mysqld(handle_fatal_signal+0x5a5)[0x5560d557e295]

/lib/x86_64-linux-gnu/libpthread.so.0(+0x12890)[0x7fa07888a890]

/lib/x86_64-linux-gnu/libc.so.6(gsignal+0xc7)[0x7fa077d9ee97]

/lib/x86_64-linux-gnu/libc.so.6(abort+0x141)[0x7fa077da0801]

mysqld(+0x497cfc)[0x5560d52cecfc]

mysqld(+0x8e6df7)[0x5560d571ddf7]

mysqld(+0x48eac7)[0x5560d52c5ac7]

mysqld(_Z17mysql_alter_tableP3THDPK25st_mysql_const_lex_stringS3_P14HA_CREATE_INFOP10TABLE_LISTP10Alter_infojP8st_orderb+0x2ee0)[0x5560d5430ce0]

mysqld(_ZN19Sql_cmd_alter_table7executeEP3THD+0x3cf)[0x5560d5480b4f]

mysqld(_Z21mysql_execute_commandP3THD+0x1226)[0x5560d53a31e6]

mysqld(_Z11mysql_parseP3THDPcjP12Parser_statebb+0x20a)[0x5560d53aaa4a]

mysqld(_Z16dispatch_command19enum_server_commandP3THDPcjbb+0x1cc7)[0x5560d53ad447]

mysqld(_Z10do_commandP3THD+0x178)[0x5560d53ae1e8]

mysqld(_Z24do_handle_one_connectionP7CONNECT+0x212)[0x5560d547dd92]

mysqld(handle_one_connection+0x3d)[0x5560d547df6d]

/lib/x86_64-linux-gnu/libpthread.so.0(+0x76db)[0x7fa07887f6db]

/lib/x86_64-linux-gnu/libc.so.6(clone+0x3f)[0x7fa077e8188f]

Trying to get some variables.

Some pointers may be invalid and cause the dump to abort.

Query (0x7fa02401b160): ALTER TABLE `atest` ADD PRIMARY KEY (`id`)

Connection ID (thread ID): 9

Status: NOT_KILLED

Optimizer switch: index_merge=on,index_merge_union=on,index_merge_sort_union=on,index_merge_intersection=on,index_merge_sort_intersection=off,engine_condition_pushdown=off,index_condition_pushdown=on,derived_merge=on,derived_with_keys=on,firstmatch=on,loosescan=on,materialization=on,in_to_exists=on,semijoin=on,partial_match_rowid_merge=on,partial_match_table_scan=on,subquery_cache=on,mrr=off,mrr_cost_based=off,mrr_sort_keys=off,outer_join_with_cache=on,semijoin_with_cache=on,join_cache_incremental=on,join_cache_hashed=on,join_cache_bka=on,optimize_join_buffer_size=off,table_elimination=on,extended_keys=on,exists_to_in=on,orderby_uses_equalities=on,condition_pushdown_for_derived=on,split_materialized=on

2019-02-24 15:57:19 0 [Note] mysqld (mysqld 10.3.13-MariaDB-1:10.3.13+maria~bionic-log) starting as process 1 ...

2019-02-24 15:57:20 0 [Warning] Setting lower_case_table_names=2 because file system for /var/lib/mysql/ is case insensitive

2019-02-24 15:57:20 0 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins

2019-02-24 15:57:20 0 [Note] InnoDB: Uses event mutexes

2019-02-24 15:57:20 0 [Note] InnoDB: Compressed tables use zlib 1.2.11

2019-02-24 15:57:20 0 [Note] InnoDB: Number of pools: 1

2019-02-24 15:57:20 0 [Note] InnoDB: Using SSE2 crc32 instructions

2019-02-24 15:57:20 0 [Note] InnoDB: Initializing buffer pool, total size = 256M, instances = 1, chunk size = 128M

2019-02-24 15:57:20 0 [Note] InnoDB: Completed initialization of buffer pool

2019-02-24 15:57:20 0 [Note] InnoDB: If the mysqld execution user is authorized, page cleaner thread priority can be changed. See the man page of setpriority().

2019-02-24 15:57:20 0 [Note] InnoDB: Starting crash recovery from checkpoint LSN=1635517

2019-02-24 15:57:20 0 [Note] InnoDB: Ignoring data file './appziodb/atest.ibd' with space ID 6. Another data file called ./appziodb/#sql-1_9.ibd exists with the same space ID.

2019-02-24 15:57:20 0 [Note] InnoDB: Ignoring data file './appziodb/atest.ibd' with space ID 5. Another data file called ./appziodb/#sql-ib21.ibd exists with the same space ID.

2019-02-24 15:57:20 0 [Note] InnoDB: Ignoring data file './appziodb/atest.ibd' with space ID 6. Another data file called ./appziodb/#sql-1_9.ibd exists with the same space ID.

2019-02-24 15:57:20 0 [ERROR] InnoDB: Operating system error number 26 in a file operation.

2019-02-24 15:57:20 0 [ERROR] InnoDB: Error number 26 means 'Text file busy'

2019-02-24 15:57:20 0 [Note] InnoDB: Some operating system error numbers are described at https://mariadb.com/kb/en/library/operating-system-error-codes/

2019-02-24 15:57:20 0 [ERROR] InnoDB: Cannot rename file './appziodb/#sql-1_9.ibd' to './appziodb/atest.ibd'

2019-02-24 15:57:20 0x7fb1da2ca7c0  InnoDB: Assertion failure in file /home/buildbot/buildbot/build/mariadb-10.3.13/storage/innobase/fil/fil0fil.cc line 2245

InnoDB: We intentionally generate a memory trap.

InnoDB: Submit a detailed bug report to https://jira.mariadb.org/

InnoDB: If you get repeated assertion failures or crashes, even

InnoDB: immediately after the mysqld startup, there may be

InnoDB: corruption in the InnoDB tablespace. Please refer to

InnoDB: https://mariadb.com/kb/en/library/innodb-recovery-modes/

InnoDB: about forcing recovery.

190224 15:57:20 [ERROR] mysqld got signal 6 ;

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: 10.3.13-MariaDB-1:10.3.13+maria~bionic-log

key_buffer_size=134217728

read_buffer_size=2097152

max_used_connections=0

max_threads=102

thread_count=0

It is possible that mysqld could use up to

key_buffer_size + (read_buffer_size + sort_buffer_size)*max_threads = 760012 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

mysqld(my_print_stacktrace+0x2e)[0x561566e4d47e]

mysqld(handle_fatal_signal+0x5a5)[0x5615668ed295]

/lib/x86_64-linux-gnu/libpthread.so.0(+0x12890)[0x7fb1d864c890]

/lib/x86_64-linux-gnu/libc.so.6(gsignal+0xc7)[0x7fb1d7b60e97]

/lib/x86_64-linux-gnu/libc.so.6(abort+0x141)[0x7fb1d7b62801]

mysqld(+0x497cfc)[0x56156663dcfc]

mysqld(+0xac3f1e)[0x561566c69f1e]

mysqld(+0x92370b)[0x561566ac970b]

mysqld(+0x92654f)[0x561566acc54f]

mysqld(+0x926a07)[0x561566acca07]

mysqld(+0x92704b)[0x561566acd04b]

mysqld(+0x927443)[0x561566acd443]

mysqld(+0x927a01)[0x561566acda01]

mysqld(+0x9d3cd1)[0x561566b79cd1]

mysqld(+0x8c6741)[0x561566a6c741]

mysqld(_Z24ha_initialize_handlertonP13st_plugin_int+0x62)[0x5615668ef8f2]

mysqld(+0x57ffa9)[0x561566725fa9]

mysqld(_Z11plugin_initPiPPci+0x85a)[0x56156672710a]

mysqld(+0x4b6df1)[0x56156665cdf1]

mysqld(_Z11mysqld_mainiPPc+0x53a)[0x56156666302a]

/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7)[0x7fb1d7b43b97]

mysqld(_start+0x2a)[0x561566655f1a]

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.

Fatal signal 11 while backtracing