InnoDB: Assertion failure in file /home/buildbot/buildbot/build/mariadb-10.3.7/storage/innobase/os/os0thread.cc line 139 during installation on Ubuntu Server 18.04 LTS as Oracle VirtualBox VM

Hello,

This fault occurs equally in both MariaDB 10.3.7 and 10.2.15 while performing the initial installation on Ubuntu Server 18.04 LTS (running as Oracle VirtualBox VM, 5 GB root partition, 2 vCores, 4 GB virtual RAM). I have reproduced the issue several times in this same environment.

The corresponding crash results on MariaDB not being properly installed and the corresponding service failing to start upon subsequent Ubuntu 18.04 reboots/startups.

Logs for both 10.3.7 and 10.2.15 attached to this Jira ticket.

If you suspect this could be related with the specific environment used, please kindly let let me know.

Thank you!

MariaDB 10.3.7:
===============
VPS System Status:
------------------
Processor(s): 2 x Intel(R) Core(TM) i7-4650U CPU @ 1.70GHz, at 2300.004 MHz, with KVM Hypervisor and full Virtualization
Linux System: Ubuntu 18.04 LTS (Bionic Beaver) x86_64 with Linux kernel 4.15.0-22-generic (#24-Ubuntu SMP Wed May 16 12:15:17 UTC 2018 )
Hostname : xcdofra1srv01, IF: enp0s3 UP, IPv4: 192.168.1.50/24, IPv6: fe80::a00:27ff:fea8:79c2/64, Ext IP: 88.18.180.185, DNS(s): 127.0.0.53
SystemLocale: LANG=en_US.UTF-8
Keyboard : PC105 ES
Date : 2018-06-03 16:56:57 CEST (Europe/Madrid), uptime 9 min, 2 users, load average: 0.00, 0.03, 0.01
Tasks : 115 total, 1 running, 61 sleeping, 0 stopped, 1 zombie
CPU(s) Usage: 2.9% User, 1.6% System, 0.4% Wait, 95.2% Idle, 100.1% Total
RAM Memory : 3.9G Total, 110M Used, 3.3G Free, 1.0M Shared, 421M Buffers+Cache, 3.5G Available
Swap File : 461M Total, 0B Used, 461M Free

Disks :
KNAME PKNAME NAME SIZE TYPE RM RO OWNER UUID MOUNTPOINT FSTYPE LABEL VENDOR MODEL
sda sda 10G disk 0 0 root ATA VBOX HARDDISK
sda1 sda |-sda1 243M part 0 0 root 8e004454-fdc6-44b7-bb8e-809a962ccba7 /boot ext2
sda2 sda |-sda2 1K part 0 0 root
sda5 sda |-sda5 4.4G part 0 0 root 14c2aa6d-42da-4c4f-bc4d-61b24f60a4f8 / ext4
sda6 sda `-sda6 5.3G part 0 0 root e9aa8b3b-8aa1-4202-89be-e784a791fef7 crypto_LUKS srv
dm-0 sda6 `-srv 5.3G crypt 0 0 root y0HEhK-UUC8-cuUT-0Mjr-vcYt-N4UF-xlGeYT LVM2_member
dm-1 dm-0 `-srvVG-srvLV 5.3G lvm 0 0 root 99f90ced-eee6-4936-a103-83b9f6b1bb4e /srv ext4

File Systems: Type IFree IUse% Size Used Avail Use% File Mounted on
/dev/sda5 ext4 164K 43% 4.3G 2.8G 1.3G 69% - /
/dev/sda1 ext2 61K 1% 236M 81M 143M 36% - /boot
/dev/mapper/srvVG-srvLV ext4 342K 1% 5.2G 22M 4.9G 1% - /srv

Network Stats: RX / TX / Total / Estimated
enp0s3:
May '18 27.81 MiB / 57.80 MiB / 85.61 MiB
Jun '18 79.44 MiB / 2.26 MiB / 81.70 MiB / 912.00 MiB
Yesterday 78.52 MiB / 2.19 MiB / 80.70 MiB
Today 947 KiB / 76 KiB / 1.00 MiB / –
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2018-06-03 16:58:07 caaa@xcdofra1srv01:~$ sudo apt-get update -y && sudo apt-get install -y mariadb-server mariadb-client

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The following additional packages will be installed:
galera-3 libaio1 libcgi-fast-perl libcgi-pm-perl libdbd-mysql-perl libdbi-perl libencode-locale-perl libfcgi-perl libhtml-parser-perl libhtml-tagset-perl
libhtml-template-perl libhttp-date-perl libhttp-message-perl libio-html-perl liblwp-mediatypes-perl libmysqlclient20 libterm-readkey-perl libtimedate-perl
liburi-perl mariadb-client-10.3 mariadb-client-core-10.3 mariadb-common mariadb-server-10.3 mariadb-server-core-10.3 mysql-common socat
Suggested packages:
libclone-perl libmldbm-perl libnet-daemon-perl libsql-statement-perl libdata-dump-perl libipc-sharedcache-perl libwww-perl mailx mariadb-test tinyca
The following NEW packages will be installed:
galera-3 libaio1 libcgi-fast-perl libcgi-pm-perl libdbd-mysql-perl libdbi-perl libencode-locale-perl libfcgi-perl libhtml-parser-perl libhtml-tagset-perl
libhtml-template-perl libhttp-date-perl libhttp-message-perl libio-html-perl liblwp-mediatypes-perl libmysqlclient20 libterm-readkey-perl libtimedate-perl
liburi-perl mariadb-client mariadb-client-10.3 mariadb-client-core-10.3 mariadb-common mariadb-server mariadb-server-10.3 mariadb-server-core-10.3 mysql-common
socat
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Preconfiguring packages ...
Package configuration Configuring mariadb-server-10.3 While not mandatory, it is highly recommended that you set a password for the MariaDB administrative "root" user. If this field is left blank, the password will not be changed. New password for the MariaDB "root" user: __________________________________________________________________________________________________________________ <Ok> *************<Ok>

Package configuration Configuring mariadb-server-10.3 Repeat password for the MariaDB "root" user: _____________________________________________ <Ok> *************<Ok>

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Setting up mariadb-server-core-10.3 (1:10.3.7+maria~bionic) ...
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Setting up libdbd-mysql-perl (4.046-1) ...
Setting up mariadb-server-10.3 (1:10.3.7+maria~bionic) ...
2018-06-03 16:59:25 0 [Note] /usr/sbin/mysqld (mysqld 10.3.7-MariaDB-1:10.3.7+maria~bionic) starting as process 3911 ...
2018-06-03 16:59:25 0 [Note] InnoDB: Using Linux native AIO
2018-06-03 16:59:25 0 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
2018-06-03 16:59:25 0 [Note] InnoDB: Uses event mutexes
2018-06-03 16:59:25 0 [Note] InnoDB: Compressed tables use zlib 1.2.11
2018-06-03 16:59:25 0 [Note] InnoDB: Number of pools: 1
2018-06-03 16:59:25 0 [Note] InnoDB: Using SSE2 crc32 instructions
2018-06-03 16:59:25 0 [Note] InnoDB: Initializing buffer pool, total size = 256M, instances = 1, chunk size = 128M
2018-06-03 16:59:25 0 [Note] InnoDB: Completed initialization of buffer pool
2018-06-03 16:59:25 0 [Note] InnoDB: If the mysqld execution user is authorized, page cleaner thread priority can be changed. See the man page of setpriority().
2018-06-03 16:59:25 0 [Note] InnoDB: Starting crash recovery from checkpoint LSN=49468
2018-06-03 16:59:26 0 [Note] InnoDB: Starting final batch to recover 13 pages from redo log.
2018-06-03 16:59:26 0 [Note] InnoDB: 128 out of 128 rollback segments are active.
2018-06-03 16:59:26 0 [Note] InnoDB: Removed temporary tablespace data file: "ibtmp1"
2018-06-03 16:59:26 0 [Note] InnoDB: Creating shared tablespace for temporary tables
2018-06-03 16:59:26 0 [Note] InnoDB: Setting file './ibtmp1' size to 12 MB. Physically writing the file full; Please wait ...
2018-06-03 16:59:26 0 [Note] InnoDB: File './ibtmp1' size is now 12 MB.
2018-06-03 16:59:26 0x7fdf617a77c0 InnoDB: Assertion failure in file /home/buildbot/buildbot/build/mariadb-10.3.7/storage/innobase/os/os0thread.cc line 139
InnoDB: Failing assertion: ret == 0
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/xtradbinnodb-recovery-modes/
InnoDB: about forcing recovery.
180603 16:59:26 [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: 10.3.7-MariaDB-1:10.3.7+maria~bionic
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 = 760011 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+0x2e)[0x562057f300fe]
/usr/sbin/mysqld(handle_fatal_signal+0x5a5)[0x5620579ce3a5]
/lib/x86_64-linux-gnu/libpthread.so.0(+0x12890)[0x7fdf5fb2f890]
/lib/x86_64-linux-gnu/libc.so.6(gsignal+0xc7)[0x7fdf5f03ee97]
/lib/x86_64-linux-gnu/libc.so.6(abort+0x141)[0x7fdf5f040801]
/usr/sbin/mysqld(+0x49cfaa)[0x562057723faa]
/usr/sbin/mysqld(+0x93a6f8)[0x562057bc16f8]
/usr/sbin/mysqld(+0x9d58f6)[0x562057c5c8f6]
/usr/sbin/mysqld(+0x8c7041)[0x562057b4e041]
/usr/sbin/mysqld(_Z24ha_initialize_handlertonP13st_plugin_int+0x62)[0x5620579d0832]
/usr/sbin/mysqld(+0x586139)[0x56205780d139]
/usr/sbin/mysqld(_Z11plugin_initPiPPci+0x85a)[0x56205780e29a]
/usr/sbin/mysqld(+0x4bd5d1)[0x5620577445d1]
/usr/sbin/mysqld(_Z11mysqld_mainiPPc+0x51b)[0x56205774a7fb]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7)[0x7fdf5f021b97]
/usr/sbin/mysqld(_start+0x2a)[0x56205773d71a]
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.
/var/lib/dpkg/info/mariadb-server-10.3.postinst: line 26: 3911 Aborted (core dumped) $MYSQL_BOOTSTRAP < $tfile
Package configuration Configuring mariadb-server-10.3 Unable to set password for the MariaDB "root" user An error occurred while setting the password for the MariaDB administrative user. This may have happened because the account already has a password, or because of a communication problem with the MariaDB server. You should check the account's password after the package installation. Please read the /usr/share/doc/mariadb-server-10.3/README.Debian file for more information. <Ok>

/var/lib/dpkg/info/mariadb-server-10.3.postinst: line 59: 3937 Done echo "$replace_query"
3938 Aborted (core dumped) | $MYSQL_BOOTSTRAP 2>&1
3939 | $ERR_LOGGER
Created symlink /etc/systemd/system/mysql.service /lib/systemd/system/mariadb.service.
Created symlink /etc/systemd/system/mysqld.service /lib/systemd/system/mariadb.service.
Created symlink /etc/systemd/system/multi-user.target.wants/mariadb.service /lib/systemd/system/mariadb.service.
Job for mariadb.service failed because the control process exited with error code.
See "systemctl status mariadb.service" and "journalctl -xe" for details.
invoke-rc.d: initscript mysql, action "start" failed.
mariadb.service - MariaDB 10.3.7 database server
Loaded: loaded (/lib/systemd/system/mariadb.service; enabled; vendor preset: enabled)
Drop-In: /etc/systemd/system/mariadb.service.d
migrated-from-my.cnf-settings.conf
Active: failed (Result: exit-code) since Sun 2018-06-03 16:59:46 CEST; 73ms ago
Docs: man:mysqld(8)
https://mariadb.com/kb/en/library/systemd/
Process: 4409 ExecStart=/usr/sbin/mysqld $MYSQLD_OPTS $_WSREP_NEW_CLUSTER $_WSREP_START_POSITION (code=exited, status=1/FAILURE)
Process: 4256 ExecStartPre=/bin/sh -c [ ! -e /usr/bin/galera_recovery ] && VAR= || VAR=`/usr/bin/galera_recovery`; [ $? -eq 0 ] && systemctl set-environment _WSREP_START_POSITION=$VAR || exit 1 (code=exited, status=0/SUCCESS)
Process: 4254 ExecStartPre=/bin/sh -c systemctl unset-environment _WSREP_START_POSITION (code=exited, status=0/SUCCESS)
Process: 4253 ExecStartPre=/usr/bin/install -m 755 -o mysql -g root -d /var/run/mysqld (code=exited, status=0/SUCCESS)
Main PID: 4409 (code=exited, status=1/FAILURE)
Status: "InnoDB 3 pages purged"

Jun 03 16:59:46 xcdofra1srv01 mysqld[4409]: 2018-06-03 16:59:46 0 [Note] InnoDB: Cannot open '/var/lib/mysql/ib_buffer_pool' for reading: No such file or directory
Jun 03 16:59:46 xcdofra1srv01 mysqld[4409]: 2018-06-03 16:59:46 0 [Note] Plugin 'FEEDBACK' is disabled.
Jun 03 16:59:46 xcdofra1srv01 mysqld[4409]: 2018-06-03 16:59:46 0 [ERROR] Could not open mysql.plugin table. Some plugins may be not loaded
Jun 03 16:59:46 xcdofra1srv01 mysqld[4409]: 2018-06-03 16:59:46 6 [Warning] Failed to load slave replication state from table mysql.gtid_slave_pos: 1146: Table 'mysql.gtid_slave_pos' doesn't exist
Jun 03 16:59:46 xcdofra1srv01 mysqld[4409]: 2018-06-03 16:59:46 0 [ERROR] Can't open and lock privilege tables: Table 'mysql.servers' doesn't exist
Jun 03 16:59:46 xcdofra1srv01 mysqld[4409]: 2018-06-03 16:59:46 0 [Note] Server socket created on IP: '127.0.0.1'.
Jun 03 16:59:46 xcdofra1srv01 mysqld[4409]: 2018-06-03 16:59:46 0 [ERROR] Fatal error: Can't open and lock privilege tables: Table 'mysql.user' doesn't exist
Jun 03 16:59:46 xcdofra1srv01 systemd[1]: mariadb.service: Main process exited, code=exited, status=1/FAILURE
Jun 03 16:59:46 xcdofra1srv01 systemd[1]: mariadb.service: Failed with result 'exit-code'.
Jun 03 16:59:46 xcdofra1srv01 systemd[1]: Failed to start MariaDB 10.3.7 database server.
dpkg: error processing package mariadb-server-10.3 (--configure):
installed mariadb-server-10.3 package post-installation script subprocess returned error exit status 1
dpkg: dependency problems prevent configuration of mariadb-server:
mariadb-server depends on mariadb-server-10.3 (>= 1:10.3.7+maria~bionic); however:
Package mariadb-server-10.3 is not configured yet.

dpkg: error processing package mariadb-server (--configure):
dependency problems - leaving unconfigured
Processing triggers for libc-bin (2.27-3ubuntu1) ...
No apport report written because the error message indicates its a followup error from a previous failure.
Processing triggers for ureadahead (0.100.0-20) ...
Processing triggers for systemd (237-3ubuntu10) ...
Errors were encountered while processing:
mariadb-server-10.3
mariadb-server
E: Sub-process /usr/bin/dpkg returned an error code (1)
2018-06-03 16:59:52 caaa@xcdofra1srv01:~$
2018-06-03 17:00:44 caaa@xcdofra1srv01:~$ dfl
Filesystem Type IFree IUse% Size Used Avail Use% File Mounted on
/dev/mapper/srvVG-srvLV ext4 342K 1% 5.2G 22M 4.9G 1% - /srv
/dev/sda1 ext2 61K 1% 236M 81M 143M 36% - /boot
/dev/sda5 ext4 163K 43% 4.3G 3.1G 988M 77% - /
tmpfs tmpfs 493K 1% 395M 720K 394M 1% - /run
tmpfs tmpfs 494K 1% 2.0G 0 2.0G 0% - /dev/shm
tmpfs tmpfs 494K 1% 2.0G 0 2.0G 0% - /sys/fs/cgroup
tmpfs tmpfs 494K 1% 395M 0 395M 0% - /run/user/1001
tmpfs tmpfs 494K 1% 5.0M 0 5.0M 0% - /run/lock
udev devtmpfs 486K 1% 1.9G 0 1.9G 0% - /dev