Azure Database for MySQL
An Azure managed MySQL database service for app development and deployment.
MySQL Error (2006) - Server Timeout on DELETE Operation in Azure Database
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Mingqi Cai
0
Reputation points
I am encountering an issue with a DELETE operation in my MySQL database hosted on Azure. The query DELETE FROM recommend_tag_new is causing a timeout, and I receive the following error:
(pymysql.err.OperationalError) (2006, "MySQL server has gone away (TimeoutError(110, 'Connection timed out'))")
The error occurs at 1:30 AM (on 8/31/2025), and this is impacting the ability to delete records from the specified table. The query is failing with the following traceback:
[SQL: DELETE FROM recommend_tag_new]
Error: (pymysql.err.OperationalError) (2006, "MySQL server has gone away (TimeoutError(110, 'Connection timed out'))")
As additional information,
the same issue previously discussed in the Microsoft Q&A thread: Microsoft Learn. This error, (pymysql.err.OperationalError) (2006, "MySQL server has gone away (TimeoutError(110, 'Connection timed out'))"), often arises during scheduled batch jobs in Azure Database for MariaDB.
And recently we had finished the migration from MariaDB to MySQL that we thought the migration could help us solve this issue but it didn't.
MySQL Timeout Settings:
SELECT @@wait_timeout, @@net_read_timeout, @@net_write_timeout, @@interactive_timeout;
# the result like:
wait_timeout = 28800
interactive_timeout = 28800
net_read_timeout = 120
net_write_timeout = 240
how often the error happened below:
Azure Database for MySQL
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Saraswathi Devadula 13,485 Reputation points Microsoft External Staff Moderator2025-09-02T07:42:57.4533333+00:00 Hello Mingqi Cai
Kindly please share the details requested in the private message for further troubleshooting.
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![](data:image/svg+xml, %3Csvg xmlns='http://www.w3.org/2000/svg' height='64' class='font-weight-bold' style='font: 600 30.11764705882353px "SegoeUI", Arial' width='64'%3E%3Ccircle fill='hsl(0, 59%, 10%)' cx='32' cy='32' r='32' /%3E%3Ctext x='50%25' y='55%25' dominant-baseline='middle' text-anchor='middle' fill='%23FFF' %3EJM%3C/text%3E%3C/svg%3E)
JananiRamesh-MSFT 29,436 Reputation points Moderator2025-09-03T04:09:38.3566667+00:00 @Mingqi Cai Thanks for your patience! "MySQL server has gone away" is a pretty generic error and can happen because of a server error or a client-side error. While Azure has automated bots which are used to detect and address server-side issues, below are the possible reason for client-side intermittent issues that can cause this error
Server dropped an incorrect or too large packet
Please increase the value for “max_allowed_packet” from the Azure Database for MySQL server parameter pane to avoid issues due to the size of the packet
Screenshot displaying server parameters for MySQL configuration in a database management interface. The highlighted parameters include
group_concat_max_lenwith a value of 1024,innodb_online_alter_log_max_sizewith a value of 134217728,max_allowed_packetset to 536870912,max_connect_errorsat 100, andmax_length_for_sort_dataalso set to 1024. Notably, themax_allowed_packetparameter is emphasized as it pertains to one of the common causes of the "MySQL server has gone away" error.Timeout:
You got a timeout from the TCP/IP connection on the client side. Please note that there are a number of parameters that can cause this timeout to happen. After the server waits for activity to happen, a number of seconds before it closes the connection, all these parameters can be edited from the Azure MySQL server parameters pane as the following.
Screenshot displaying configuration settings for MySQL server parameters with a focus on timeout values. The highlighted parameters include various timeout settings such as
innodb_lock_wait_timeout,interactive_timeout,lock_wait_timeout,net_read_timeout,net_write_timeout,slave_net_timeout, andwait_timeout. The settings are part of the server parameters section, indicating values for timeout durations that could affect the stability and connectivity of the MySQL server, potentially linked to encountering the "MySQL server has gone away" error intermittently.Killing a running process
DBA killed the running thread with a KILL statement or a mysqladmin kill
Already Closed connection with the database
You tried to run a query after closing the connection to the server. This indicates a logic error in the application that should be corrected.
Reference:
https://dev.mysql.com/doc/refman/5.7/en/gone-away.html
If you have any further questions or need additional assistance, feel free to ask!
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Mingqi Cai 0 Reputation points
2025-09-04T02:21:47.18+00:00 Thank you for following up. I tried the setting you mentioned, and it looks good now. Since the issue used to happen irregularly, I’ll need a bit more time to confirm.
If there are any new updates, I will comment here as soon as I can.
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JananiRamesh-MSFT 29,436 Reputation points Moderator
2025-09-04T04:14:19.8166667+00:00 Mingqi Cai Thanks for the update! Sure, feel free to reach-out if you encounter the same issue in future. We would be happy to help.
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Mingqi Cai 0 Reputation points
2025-09-05T00:53:45.45+00:00 The same issue occurred again today. The previous occurrence was on August 31st.
Thank you for your assistance, and please let me know if you need any additional information.
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JananiRamesh-MSFT 29,436 Reputation points Moderator
2025-09-08T08:47:33.18+00:00 @Mingqi Cai Thanks for getting back, as the issue is intermittent this would need 1:1 connect to troubleshoot further Kindly share the details requested in the private message
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