# Issues with Mysql/InnoDB after Bullseye migration
**URL:** https://forum.yunohost.org/t/issues-with-mysql-innodb-after-bullseye-migration/20969
**Category:** Support
**Created:** [August 29, 2022, 5:23pm UTC](https://forum.yunohost.org/t/issues-with-mysql-innodb-after-bullseye-migration/20969 "2022-08-29T17:23:32Z")
**Posts on this page:** 19
**Page:** 1
### Author:  [@Lapineige](https://forum.yunohost.org/u/Lapineige)
#### Post date: [August 16, 2022, 10:37am UTC](https://forum.yunohost.org/t/issues-with-mysql-innodb-after-bullseye-migration/20969/1 "2022-08-16T10:37:19Z")
Pour ma part le problème avec la migration Postgresql11→13 a été résolu simplement, en suivant vos conseils : j’ai supprimé les 4 paquets PostgreSQL11 qui gênaient, car aucune application de les utilisait.
C’est passé sans ce soucis cette fois 🙂 (sur un Raspberry Pi 4).
* * *
Par contre le problème de Mysql et Nextcloud reste présent, Nextcloud ne fonctionne plus à cause de cela ☹
Je ne peux pas non plus faire la mise à jour de Nextcloud 22.2.7~ynh1 à 22.2.10~ynh1.
edit:
Un `service mysql status` donne:
> [ERROR] InnoDB: Space id and page no stored in the page, read in are [page id: space=2688, page number=200800], should be [page id: space=2688, page number=3608672]
FreshRSS fonctionne, et utilise aussi MySQL 🤔
edit 2 : J’ai essayé de me connecter à la base de donnée avec `ynh_mysql_connect_as`, ça mouline dans le vide jusqu’au timeout.
edit3: le fichier `nextcloud.log` ne rapporte rien quand j’essaye de me connecter via mon navigateur (qui donne un 504 Gateway time-out).
edit 4 : après un nouvel essai de redémarrage de php7.4-fpm, maintenant j’ai une Internal Server Error pour Nextcloud, et pour mariadb (mysql) ce message d’erreur:
> mariadb.service: Main process exited, code=killed, status=6/ABRT
> ░░ Subject: Unit process exited
> ░░ Defined-By: systemd
> ░░ Support: [Debian -- User Support](https://www.debian.org/support)
> ░░
> ░░ An ExecStart= process belonging to unit mariadb.service has exited.
> ░░
> ░░ The process’ exit code is ‘killed’ and its exit status is 6.
> ░░ systemd[1]: mariadb.service: Failed with result ‘signal’.
> ░░ Subject: Unit failed
> ░░ Defined-By: systemd
> ░░ Support: [Debian -- User Support](https://www.debian.org/support)
> ░░
> ░░ The unit mariadb.service has entered the ‘failed’ state with result ‘signal’.
edit 5 : more detailed logs from journalctl.
A bunch of several times :
> août 14 15:40:44 --Thread 2565497728 has waited at row0sel.cc line 4718 for 11.00 seconds the semaphore:
> août 14 15:40:44 S-lock on RW-latch at 0x9cb54e8c created in file buf0buf.cc line 1226
> août 14 15:40:44 a writer (thread id 2594022272) has reserved it in mode wait exclusive
> août 14 15:40:44 number of readers 1, waiters flag 1, lock\_word: ffffffff
> août 14 15:40:44 Last time write locked in file buf0rea.cc line 120
> août 14 15:40:44 InnoDB: Pending reads 0, writes 0
And then
> août 14 15:40:44 2022-08-14 15:40:44 0 [ERROR] [FATAL] InnoDB: Semaphore wait has lasted \> 600 seconds. We intentionally crash the server because it appears to be hung.
> août 14 15:40:44 220814 15:40:44 [ERROR] mysqld got signal 6 ;
> août 14 15:40:44 This could be because you hit a bug. It is also possible that this binary
> août 14 15:40:44 or one of the libraries it was linked against is corrupt, improperly built,
> août 14 15:40:44 or misconfigured. This error can also be caused by malfunctioning hardware.
> août 14 15:40:44 To report this bug, see [MariaDB Community Bug Reporting - MariaDB Knowledge Base](https://mariadb.com/kb/en/reporting-bugs)
> août 14 15:40:44 We will try our best to scrape up some info that will hopefully help
> août 14 15:40:44 diagnose the problem, but since we have already crashed,
> août 14 15:40:44 something is definitely wrong and this may fail.
> août 14 15:40:44 Server version: 10.5.15-MariaDB-0+deb11u1
---
### Author:  [@Lapineige](https://forum.yunohost.org/u/Lapineige)
#### Post date: [August 16, 2022, 10:37am UTC](https://forum.yunohost.org/t/issues-with-mysql-innodb-after-bullseye-migration/20969/2 "2022-08-16T10:37:19Z")
> [@Lapineige](#):
>
> [ERROR] [FATAL] InnoDB: Semaphore wait has lasted \> 600 seconds. We intentionally crash the server because it appears to be hung.
Should I try to increase InnoDB timeout settings ? (and some related settings ?)
---
### Author:  [@Lapineige](https://forum.yunohost.org/u/Lapineige)
#### Post date: [August 29, 2022, 5:23pm UTC](https://forum.yunohost.org/t/issues-with-mysql-innodb-after-bullseye-migration/20969/3 "2022-08-29T17:23:32Z")
Update on my issue: server crashed during weekly backup, before of MySQL server error during wallabag backup (but wallabag an freshRSS where working properly using Mysql DB (??) before, while Nextcloud did not).
To elaborate on that: based on archivist email, I can see two errors : first Nextcloud backup fails with `Lost connection to MySQL server during query (2013)` then Wallabag backup fails with `Can't connect to local MySQL server through socket '/run/mysqld/mysqld.sock' (111)" when trying to connect`.
Well, actually it didn’t crash: it sent me an email hours after that. I’m still receiving emails from time to time. It even auto update itselfs (I’m receiving emails with new package to update, and they change over time).
But no web app is responding and SSH doesn’t work (`kex_exchange_identification: read: Connection reset by peer `). Same as after a reboot.
* * *
* * *
* * *
Can some moderator split my post into another topic ? I would generate less noise here and maybe get more attention on that specific issue. Thanks ! 🙂
---
### Author:  [@Aleks](https://forum.yunohost.org/u/Aleks)
#### Post date: [August 29, 2022, 6:20pm UTC](https://forum.yunohost.org/t/issues-with-mysql-innodb-after-bullseye-migration/20969/4 "2022-08-29T18:20:45Z")
> [@Lapineige](#):
>
> Can some moderator split my post into another topic ? I would generate less noise here and maybe get more attention on that specific issue. Thanks !
Done even though I’m a bit lost in the discussion / not sure to understand what’s broken excatly 😅
---
### Author:  [@Lapineige](https://forum.yunohost.org/u/Lapineige)
#### Post date: [August 29, 2022, 8:02pm UTC](https://forum.yunohost.org/t/issues-with-mysql-innodb-after-bullseye-migration/20969/5 "2022-08-29T20:02:38Z")
You rocks 😃
Well, to summarize: after migration, Mysql server has issues, and gives a timeout.
This will result in a failed reboot, with no ssh access (hence in a dead server).
Nextcloud can’t work because of that, FreshRSS and Wallabag can until you backup them (msqldump fails).
---
### Author:  [@Lapineige](https://forum.yunohost.org/u/Lapineige)
#### Post date: [September 9, 2022, 9:41am UTC](https://forum.yunohost.org/t/issues-with-mysql-innodb-after-bullseye-migration/20969/6 "2022-09-09T09:41:00Z")
After the crash I mentioned (caused by this issue), I restored a backup from before Bulleyes migration.
I will try again and let you know…
> [@Lapineige](#):
>
> Well, actually it didn’t crash: it sent me an email hours after that. I’m still receiving emails from time to time. It even auto update itselfs (I’m receiving emails with new package to update, and they change over time).
> But no web app is responding and SSH doesn’t work (`kex_exchange_identification: read: Connection reset by peer `). Same as after a reboot.
I have an hint about that: server IP changed for some unknown reason. That might explain why I had no access.
---
### Author:  [@Lapineige](https://forum.yunohost.org/u/Lapineige)
#### Post date: [September 9, 2022, 11:54am UTC](https://forum.yunohost.org/t/issues-with-mysql-innodb-after-bullseye-migration/20969/7 "2022-09-09T11:54:12Z")
Nextcloud Internal Server error again.
Not sure if I have the same mysql server error, but `services mysql status` gives:
```auto
Loaded: loaded (/lib/systemd/system/mariadb.service; enabled; vendor preset: enabled)
Active: active (running) since Fri 2022-09-09 13:50:51 CEST; 32s ago
Docs: man:mariadbd(8)
https://mariadb.com/kb/en/library/systemd/
Process: 8445 ExecStartPre=/usr/bin/install -m 755 -o mysql -g root -d /var/run/mysqld (code=exited, status=0/SUCCESS)
Process: 8447 ExecStartPre=/bin/sh -c systemctl unset-environment _WSREP_START_POSITION (code=exited, status=0/SUCCESS)
Process: 8449 ExecStartPre=/bin/sh -c [! -e /usr/bin/galera_recovery] && VAR= || VAR=`cd /usr/bin/..; /usr/bin/galera_recovery`; [$? -eq 0] && systemctl set-environment _WSREP_START_POSITION=$VAR || exit 1 (code=exited, status=0/SUCCESS)
Process: 8516 ExecStartPost=/bin/sh -c systemctl unset-environment _WSREP_START_POSITION (code=exited, status=0/SUCCESS)
Process: 8518 ExecStartPost=/etc/mysql/debian-start (code=exited, status=0/SUCCESS)
Main PID: 8496 (mariadbd)
Status: "Taking your SQL requests now..."
Tasks: 20 (limit: 4915)
CGroup: /system.slice/mariadb.service
└─8496 /usr/sbin/mariadbd
mariadbd[8496]: 2022-09-09 13:50:52 0 [ERROR] InnoDB: Space id and page no stored in the page, read in are [page id: space=2688, page number=198698], should be [page id: space=2688, page number=3606570]
```
(multiple times)
---
### Author:  [@Lapineige](https://forum.yunohost.org/u/Lapineige)
#### Post date: [September 9, 2022, 5:34pm UTC](https://forum.yunohost.org/t/issues-with-mysql-innodb-after-bullseye-migration/20969/8 "2022-09-09T17:34:53Z")
If I try to backup Nextcloud:
`mysqldump: Couldn't execute 'SELECT /*!40001 SQL_NO_CACHE */ `fileid`, `storage`, `path`, `path\_hash`, `parent`, `name`, `mimetype`, `mimepart`, `size`, `mtime`, `storage\_mtime`, `encrypted`, `unencrypted\_size`, `etag`, `permissions`, `checksum`FROM`oc\_filecache`': Lost connection to MySQL server during query (2013)`
A FreshRSS backup works. It does a mysqldump too if I’m not wrong…
WTF is happening to that mysql server, that if not responding for one apps but does for the others ??
---
### Author:  [@Lapineige](https://forum.yunohost.org/u/Lapineige)
#### Post date: [September 9, 2022, 5:39pm UTC](https://forum.yunohost.org/t/issues-with-mysql-innodb-after-bullseye-migration/20969/9 "2022-09-09T17:39:18Z")
If I try to stop (then restart) MySQL service :
`Stopping MariaDB 10.5.15 database server... sept. 09 19:36:04 yunohost.lapineige.fr mariadbd[27855]: 2022-09-09 19:36:04 0 [Warning] /usr/sbin/mariadbd: Thread 31 (user : 'nextcloud') did not exit `
Soooo… Nextcloud user got deleted ???
Should I try to regenerate mysql conf ?
* * *
edit : stopping the serviced failed (it timed out). Full log : [sept. 09 19:36:04 mariadbd[27855]: 2022-09-09 19:36:04 0 [Warning] /usr/sbin/ma - Pastebin.com](https://pastebin.com/UGrq1mK1)
But I can start it ! (Nextcloud still fails)
---
### Author:  [@Lapineige](https://forum.yunohost.org/u/Lapineige)
#### Post date: [September 16, 2022, 5:18pm UTC](https://forum.yunohost.org/t/issues-with-mysql-innodb-after-bullseye-migration/20969/10 "2022-09-16T17:18:47Z")
🆙
Any idea ? 😅
---
### Author:  [@huha](https://forum.yunohost.org/u/huha)
#### Post date: [September 18, 2022, 4:21pm UTC](https://forum.yunohost.org/t/issues-with-mysql-innodb-after-bullseye-migration/20969/11 "2022-09-18T16:21:56Z")
**Edit:** _Moved the whole post to [here](https://forum.yunohost.org/t/mysql-service-keeps-stopping/21243/2) as suggested by @Lapineige._ thx!
---
### Author:  [@Lapineige](https://forum.yunohost.org/u/Lapineige)
#### Post date: [September 20, 2022, 4:50pm UTC](https://forum.yunohost.org/t/issues-with-mysql-innodb-after-bullseye-migration/20969/12 "2022-09-20T16:50:20Z")
This looks like a different issue, where your server run out of memory.
See: [Mysql service keeps stopping - #2 by Aleks](https://forum.yunohost.org/t/mysql-service-keeps-stopping/21243/2)
---
### Author:  [@wbk](https://forum.yunohost.org/u/wbk)
#### Post date: [September 20, 2022, 6:20pm UTC](https://forum.yunohost.org/t/issues-with-mysql-innodb-after-bullseye-migration/20969/13 "2022-09-20T18:20:13Z")
> [@Lapineige](#):
>
> ```auto
> mariadbd[8496]: 2022-09-09 13:50:52 0 [ERROR] InnoDB: Space id and page no stored in the page, read in are [page id: space=2688, page number=198698], should be [page id: space=2688, page number=3606570]
>
> ```
>
> (multiple times)
Here it mentions `page number=198698` should be `page number=3606570`. Is that the same for each log record?
Could some DB’s or tables have been corrupted? If FreshRSS is a backup at filesystem level or block level, it does not know about MySQL transactions (and MySQL does not know about a running backup). That doesn’t help you much further, but could explain why some apps do work, and others don’t.
---
### Author:  [@Lapineige](https://forum.yunohost.org/u/Lapineige)
#### Post date: [September 22, 2022, 11:29am UTC](https://forum.yunohost.org/t/issues-with-mysql-innodb-after-bullseye-migration/20969/14 "2022-09-22T11:29:42Z")
I just had a look, there is a bunch of them:
```auto
[ERROR] InnoDB: Space id and page no stored in the page, read in are [page id: space=2688, page number=200810], should be [page id: space=2688, page number=3608682]`
page number=3607443]
[ERROR] InnoDB: Space id and page no stored in the page, read in are [page id: space=2688, page number=200799], should be [page id: space=268
8, page number=3608671]
[ERROR] InnoDB: Space id and page no stored in the page, read in are [page id: space=2688, page number=200800], should be [page id: space=268
8, page number=3608672]
[ERROR] InnoDB: Space id and page no stored in the page, read in are [page id: space=2688, page number=200801], should be [page id: space=268
8, page number=3608673]
[ERROR] InnoDB: Space id and page no stored in the page, read in are [page id: space=2688, page number=200806], should be [page id: space=268
8, page number=3608678]
[ERROR] InnoDB: Space id and page no stored in the page, read in are [page id: space=2688, page number=200808], should be [page id: space=268
8, page number=3608680]
[ERROR] InnoDB: Space id and page no stored in the page, read in are [page id: space=2688, page number=200809], should be [page id: space=268
8, page number=3608681]
[ERROR] InnoDB: Space id and page no stored in the page, read in are [page id: space=2688, page number=200810], should be [page id: space=268
8, page number=3608682]
```
So it’s not the same one.
Also I noticed something else : If I try to load Nextcloud web page, it takes time without responding, and then Internal server error.
And… in fact Mysql service crash in the mid-time. It restarts with this error (I did not see it in the log before this restart).
---
### Author:  [@Lapineige](https://forum.yunohost.org/u/Lapineige)
#### Post date: [September 22, 2022, 12:34pm UTC](https://forum.yunohost.org/t/issues-with-mysql-innodb-after-bullseye-migration/20969/15 "2022-09-22T12:34:31Z")
I’m making some progress: I searched for that error message, I found `mysqlcheck` command.
This can check and repair tables.
I did this for owncloud.
It worked… until it failed after the table `nextcloud.oc_file_locks`
```auto
[a whole set of line looking the same of the next 3]
nextcloud.oc_file_locks
note : Table does not support optimize, doing recreate + analyze instead
status : OK
mysqlcheck: Got error: 2013: Lost connection to MySQL server during query when executing 'OPTIMIZE TABLE ... '
```
Listing the table, it seems that the next one is `oc_filecache`
If I try to “mysqlcheck” it, if fails with the above error `mysqlcheck: Got error: Lost connection to MySQL server during query when executing 'OPTIMIZE TABLE ... '`.
I wonder what I could do to fix that table, if it fails before starting 🤔
Should I drop it ?
---
### Author:  [@Lapineige](https://forum.yunohost.org/u/Lapineige)
#### Post date: [September 22, 2022, 1:02pm UTC](https://forum.yunohost.org/t/issues-with-mysql-innodb-after-bullseye-migration/20969/16 "2022-09-22T13:02:32Z")
```auto
DROP TABLE `oc_filecache`;
ERROR 2006 (HY000): MySQL server has gone away
No connection. Trying to reconnect...
Connection id: 30
Current database: nextcloud
Query OK, 0 rows affected (3 min 36.341 sec)
```
Fail ☹
edit : It dropped it in fact. It does not solve the issue.
---
### Author:  [@Lapineige](https://forum.yunohost.org/u/Lapineige)
#### Post date: [September 22, 2022, 2:33pm UTC](https://forum.yunohost.org/t/issues-with-mysql-innodb-after-bullseye-migration/20969/17 "2022-09-22T14:33:14Z")
I solved it ! 🎉
Also mysqldump can’t work because of the crashing server.
Honestly I didn’t really know what I where doing, the consequences and so on, but:
- Diagnosis : `oc_filecache` was corrupted in some way.
- How I solved it:
- `mysql` → `use nextcloud` → `DROP oc_filecache` to remove that broken table (the content does not really matters in that case)
- recreate the table:
```auto
CREATE TABLE oc_filecache (
fileid bigint(20) NOT NULL AUTO_INCREMENT,
storage bigint(20) NOT NULL DEFAULT 0,
path varchar(4000) DEFAULT NULL,
path_hash varchar(32) NOT NULL,
parent bigint(20) NOT NULL DEFAULT 0,
name varchar(250) DEFAULT NULL,
mimetype bigint(20) NOT NULL DEFAULT 0,
mimepart bigint(20) NOT NULL DEFAULT 0,
size bigint(20) NOT NULL DEFAULT 0,
mtime bigint(20) NOT NULL DEFAULT 0,
storage_mtime bigint(20) NOT NULL DEFAULT 0,
encrypted int(11) NOT NULL DEFAULT 0,
unencrypted_size bigint(20) NOT NULL DEFAULT 0,
etag varchar(40) DEFAULT NULL,
permissions int(11) DEFAULT 0,
checksum varchar(255) DEFAULT NULL,
index(storage),
index(parent),
index(size),
index(mtime),
PRIMARY KEY (fileid)
)
ENGINE=INNODB;
```
How I knew that ? (guessed it in fact…)
I logged in another server with a working Nextcloud. Then in mysql, `describe oc_filecache` gives all the information about the tables formatting and so on.
- Then in `/var/www/nextcloud`, I ran `sudo -u nextcloud php7.4 occ files:cleanup`. I don’t really know what it does, but I believe it populates the cache again or something like that.
Then Nextcloud is working.
---
### Author:  [@Lapineige](https://forum.yunohost.org/u/Lapineige)
#### Post date: [September 22, 2022, 2:52pm UTC](https://forum.yunohost.org/t/issues-with-mysql-innodb-after-bullseye-migration/20969/18 "2022-09-22T14:52:15Z")
`[ERROR] InnoDB: Space id and page no stored in the page, read in are [page id: space=2688, page number=200806], should be [page id: space=2688, page number=3608678]` errors are still here, but well, it works 🤔
---
### Author:  [@system](https://forum.yunohost.org/u/system)
#### Post date: [October 22, 2022, 2:53pm UTC](https://forum.yunohost.org/t/issues-with-mysql-innodb-after-bullseye-migration/20969/19 "2022-10-22T14:53:01Z")
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