Worpress (really) self-hosted : mysql issue - php

Question

I have made a Wordpress website first hosted locally with local by Flywheel.
I am trying to fully self-host it with a personal server (running ubuntu 18.04), not using some online ftp. I have found no documentation online about the way to do it, only people trying to sell theirs ftp services with a ready-to-use Wordpress environment... I managed to install some things, and when I enter the static IP address of the website, it works!
The problem:
After some time, a message like this appears : Error while trying to connect to the database and the website is down.
If I run /etc/init.d/mysql start again, the website works again! 30 min later, it breaks again, displaying the message above...
This is what I have done:
I used Duplicator to made an image of the website, and transferred it to the server.
I have installed:
nginx (for reverse proxy)
php 7.2
mysql-server
mysql-client
php7.2-mysql and some other extensions
My logins in wp-config.php are correct
Can you help me please ?
Things that failed:
restarting the server and reinstall everything
sudo systemctl reload mysql
Failed to reload mysql.service: Job type reload is not applicable for unit mysql.service.
See system logs and 'systemctl status mysql.service' for details.
sudo systemctl force-reload mysql
Job for mysql.service failed because the control process exited with error code.
See "systemctl status mysql.service" and "journalctl -xe" for details.
systemctl status mysql.service
mysql.service - MySQL Community Server
Loaded: loaded (/lib/systemd/system/mysql.service; enabled; vendor preset: enabled)
Active: failed (Result: exit-code) since Wed 2020-04-22 10:07:23 UTC; 24min ago
Process: 10681 ExecStart=/usr/sbin/mysqld —daemonize —pid-file=/run/mysqld/mysqld.pid (code=exited, status=1/FAILURE)
Process: 10659 ExecStartPre=/usr/share/mysql/mysql-systemd-start pre (code=exited, status=0/SUCCESS)
Main PID: 10433 (code=exited, status=0/SUCCESS)
Apr 22 10:07:23 ewenvm systemd[1]: mysql.service: Failed with result 'exit-code'.
Apr 22 10:07:23 ewenvm systemd[1]: Failed to start MySQL Community Server.
Apr 22 10:07:23 ewenvm systemd[1]: mysql.service: Service hold-off time over, scheduling restart.
Apr 22 10:07:23 ewenvm systemd[1]: mysql.service: Scheduled restart job, restart counter is at 5.
Apr 22 10:07:23 ewenvm systemd[1]: Stopped MySQL Community Server.
Apr 22 10:07:23 ewenvm systemd[1]: mysql.service: Start request repeated too quickly.
Apr 22 10:07:23 ewenvm systemd[1]: mysql.service: Failed with result 'exit-code'.
Apr 22 10:07:23 ewenvm systemd[1]: Failed to start MySQL Community Server.
journalctl -xe
— Support: http://www.ubuntu.com/support
—
— Unit mysql.service has failed.
—
— The result is RESULT.
Apr 22 10:07:23 name-of-my-server systemd[1]: mysql.service: Service hold-off time over, scheduling restart.
Apr 22 10:07:23 name-of-my-server systemd[1]: mysql.service: Scheduled restart job, restart counter is at 5.
— Subject: Automatic restarting of a unit has been scheduled
— Defined-By: systemd
— Support: http://www.ubuntu.com/support
—
— Automatic restarting of the unit mysql.service has been scheduled, as the result for
— the configured Restart= setting for the unit.
Apr 22 10:07:23 name-of-my-server systemd[1]: Stopped MySQL Community Server.
— Subject: Unit mysql.service has finished shutting down
— Defined-By: systemd
— Support: http://www.ubuntu.com/support
—
— Unit mysql.service has finished shutting down.
Apr 22 10:07:23 name-of-my-server systemd[1]: mysql.service: Start request repeated too quickly.
Apr 22 10:07:23 name-of-my-server systemd[1]: mysql.service: Failed with result 'exit-code'.
Apr 22 10:07:23 name-of-my-server systemd[1]: Failed to start MySQL Community Server.
— Subject: Unit mysql.service has failed
— Defined-By: systemd
— Support: http://www.ubuntu.com/support
—
— Unit mysql.service has failed.
—
— The result is RESULT.
Apr 22 10:09:01 name-of-my-server CRON[10701]: pam_unix(cron:session): session opened for user root by (uid=0)
Apr 22 10:09:01 name-of-my-server CRON[10702]: (root) CMD ( [ -x /usr/lib/php/sessionclean ] && if [ ! -d /run/systemd/system ]; then /usr/lib/php/sessionclean; fi)
Apr 22 10:09:01 name-of-my-server CRON[10701]: pam_unix(cron:session): session closed for user root
Apr 22 10:09:03 name-of-my-server systemd[1]: Starting Clean php session files...
— Subject: Unit phpsessionclean.service has begun start-up
— Defined-By: systemd
— Support: http://www.ubuntu.com/support
—
— Unit phpsessionclean.service has begun starting up.
Apr 22 10:09:04 name-of-my-server systemd[1]: Started Clean php session files.
— Subject: Unit phpsessionclean.service has finished start-up
— Defined-By: systemd
— Support: http://www.ubuntu.com/support
—
— Unit phpsessionclean.service has finished starting up.
—
— The start-up result is RESULT.
Apr 22 10:13:11 name-of-my-server sshd[10770]: Did not receive identification string from 182.182.22.159 port 52155
Apr 22 10:15:31 name-of-my-server systemd-timesyncd[2721]: Timed out waiting for reply from 91.189.89.199:123 (ntp.ubuntu.com).
Apr 22 10:15:41 name-of-my-server systemd-timesyncd[2721]: Timed out waiting for reply from 91.189.89.198:123 (ntp.ubuntu.com).
Apr 22 10:15:51 name-of-my-server systemd-timesyncd[2721]: Timed out waiting for reply from 91.189.91.157:123 (ntp.ubuntu.com).
Apr 22 10:16:01 name-of-my-server systemd-timesyncd[2721]: Timed out waiting for reply from 91.189.94.4:123 (ntp.ubuntu.com).
Apr 22 10:17:01 name-of-my-server CRON[10779]: pam_unix(cron:session): session opened for user root by (uid=0)
Apr 22 10:17:01 name-of-my-server CRON[10780]: (root) CMD ( cd / && run-parts —report /etc/cron.hourly)
Apr 22 10:17:01 name-of-my-server CRON[10779]: pam_unix(cron:session): session closed for user root
Here are the logs in /var/log/mysql/error/log :
2020-04-22T09:46:51.409203Z 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use —explicit_defaults_for_timestamp server option (see documentation for more details).
2020-04-22T09:46:51.413886Z 0 [Note] /usr/sbin/mysqld (mysqld 5.7.29-0ubuntu0.18.04.1) starting as process 10312 ...
2020-04-22T09:46:51.480012Z 0 [Note] InnoDB: PUNCH HOLE support available
2020-04-22T09:46:51.480056Z 0 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
2020-04-22T09:46:51.480062Z 0 [Note] InnoDB: Uses event mutexes
2020-04-22T09:46:51.480079Z 0 [Note] InnoDB: GCC builtin __atomic_thread_fence() is used for memory barrier
2020-04-22T09:46:51.480086Z 0 [Note] InnoDB: Compressed tables use zlib 1.2.11
2020-04-22T09:46:51.480091Z 0 [Note] InnoDB: Using Linux native AIO
2020-04-22T09:46:51.480890Z 0 [Note] InnoDB: Number of pools: 1
2020-04-22T09:46:51.481899Z 0 [Note] InnoDB: Using CPU crc32 instructions
2020-04-22T09:46:51.487169Z 0 [Note] InnoDB: Initializing buffer pool, total size = 128M, instances = 1, chunk size = 128M
2020-04-22T09:46:51.490733Z 0 [ERROR] InnoDB: mmap(137428992 bytes) failed; errno 12
2020-04-22T09:46:51.490760Z 0 [ERROR] InnoDB: Cannot allocate memory for the buffer pool
2020-04-22T09:46:51.490768Z 0 [ERROR] InnoDB: Plugin initialization aborted with error Generic error
2020-04-22T09:46:51.490778Z 0 [ERROR] Plugin 'InnoDB' init function returned error.
2020-04-22T09:46:51.492322Z 0 [ERROR] Plugin 'InnoDB' registration as a STORAGE ENGINE failed.
2020-04-22T09:46:51.492337Z 0 [ERROR] Failed to initialize builtin plugins.
2020-04-22T09:46:51.492342Z 0 [ERROR] Aborting
2020-04-22T09:46:51.494236Z 0 [Note] Binlog end
2020-04-22T09:46:51.495643Z 0 [Note] Shutting down plugin 'CSV'
2020-04-22T09:46:51.508165Z 0 [Note] /usr/sbin/mysqld: Shutdown complete

Answer 1

This is strange. MySQL installed on Ubuntu with sudo apt install mysql-server is usually bulletproof.
As I read your error logs, this is the root-cause of your failures.
2020-04-22T09:46:51.490733Z 0 [ERROR] InnoDB: mmap(137 428 992 bytes) failed; errno 12
When MySQL, specifically the InnoDB "access method", was starting, it could not map 137 some-odd megabytes of memory to a file in the file system.
Do you have enough RAM on your Ubuntu instance? Is the disk or SSD almost full? If you have a separate disk partition for your /tmp directory is it big enough? (Avoid RAMDISK for /tmp when you're running MySQL.) Does it have other heavy applications running on it?
If this were my project and I was working with a VM, I would erase it and start over at this point.
I'm a big fan of Digital Ocean's step by step tutorials. I know they're a server-rental company, but their tutorials work for local installs too. https://www.digitalocean.com/community/tutorials/how-to-install-wordpress-with-lamp-on-ubuntu-18-04