Fixing "Lock wait timeout exceeded; try restarting transaction" for a 'stuck" Mysql table?

Question

From a script I sent a query like this thousands of times to my local database:

update some_table set some_column = some_value

I forgot to add the where part, so the same column was set to the same a value for all the rows in the table and this was done thousands of times and the column was indexed, so the corresponding index was probably updated too lots of times.

I noticed something was wrong, because it took too long, so I killed the script. I even rebooted my computer since then, but something stuck in the table, because simple queries take a very long time to run and when I try dropping the relevant index it fails with this message:

Lock wait timeout exceeded; try restarting transaction

It's an innodb table, so stuck the transaction is probably implicit. How can I fix this table and remove the stuck transaction from it?

Answer 1

If you're here like me with a DigitalOcean Managed Database, you can configure your MYSQL, Postgres and other database by making a request to digital ocean APIs.

The values directly relating to the timeout are: wait_timeout and interactive_timeout. both are connection types. E.g,setting both timeouts to 600 seconds (10 minutes):

Initiate a PATCH request with Header: Authorization: Bearer {{ Token }} and payload.

URL: https://api.digitalocean.com/v2/databases/{YOUR_DATABASE_CLUSER_ID}/config

{
    "config": {
        "wait_timeout": 600,
        "interactive_timeout": 600
    }
}

---

Directly managing or Using a command-line client to connect to your SQL server

SET GLOBAL wait_timeout = 600;
SET GLOBAL interactive_timeout = 600;

After setting these values, you can confirm the configuration by running:

SHOW VARIABLES LIKE 'wait_timeout';

N.B If your application uses a connection pool, ensure your application’s connection pooling settings align with your wait_timeout configuration.

Answer 2

Issue in my case: Some updates were made to some rows within a transaction and before the transaction was committed, in another place, the same rows were being updated outside this transaction. Ensuring that all the updates to the rows are made within the same transaction resolved my issue.

Answer 3

This happened to me when I was accessing the database from multiple platforms, for example from dbeaver and control panels. At some point dbeaver got stuck and therefore the other panels couldn't process additional information. The solution is to reboot all access points to the database. close them all and restart.

Answer 4

issue resolved in my case by changing delete to truncate

issue- query:

delete from Survey1.sr_survey_generic_details
mycursor.execute(query)

fix- query:

truncate table Survey1.sr_survey_generic_details
mycursor.execute(query)

Answer 5

Goto processes in mysql.

So can see there is task still working.

Kill the particular process or wait until process complete.

Answer 6

When you establish a connection for a transaction, you acquire a lock before performing the transaction. If not able to acquire the lock, then you try for sometime. If lock is still not obtainable, then lock wait time exceeded error is thrown. Why you will not able to acquire a lock is that you are not closing the connection. So, when you are trying to get a lock second time, you will not be able to acquire the lock as your previous connection is still unclosed and holding the lock.

Solution: close the connection or setAutoCommit(true) (according to your design) to release the lock.

Answer 7

This started happening to me when my database size grew and I was doing a lot of transactions on it.

Truth is there is probably some way to optimize either your queries or your DB but try these 2 queries for a work around fix.

Run this:

SET GLOBAL innodb_lock_wait_timeout = 5000; 

And then this:

SET innodb_lock_wait_timeout = 5000; 

Answer 8

You can check the currently running transactions with

SELECT * FROM `information_schema`.`innodb_trx` ORDER BY `trx_started`

Your transaction should be one of the first, because it's the oldest in the list. Now just take the value from trx_mysql_thread_id and send it the KILL command:

KILL 1234;

If you're unsure which transaction is yours, repeat the first query very often and see which transactions persist.

Answer 9

Check InnoDB status for locks

SHOW ENGINE InnoDB STATUS;

Check MySQL open tables

SHOW OPEN TABLES WHERE In_use > 0;

Check pending InnoDB transactions

SELECT * FROM `information_schema`.`innodb_trx` ORDER BY `trx_started`; 

Check lock dependency - what blocks what

SELECT * FROM `information_schema`.`innodb_locks`;

After investigating the results above, you should be able to see what is locking what.

The root cause of the issue might be in your code too - please check the related functions especially for annotations if you use JPA like Hibernate.

For example, as described here, the misuse of the following annotation might cause locks in the database:

@Transactional(propagation = Propagation.REQUIRES_NEW) 

Answer 10

I had a similar problem and solved it by checking the threads that are running. To see the running threads use the following command in mysql command line interface:

SHOW PROCESSLIST;

It can also be sent from phpMyAdmin if you don't have access to mysql command line interface.
This will display a list of threads with corresponding ids and execution time, so you can KILL the threads that are taking too much time to execute. In phpMyAdmin you will have a button for stopping threads by using KILL, if you are using command line interface just use the KILL command followed by the thread id, like in the following example:

KILL 115;

This will terminate the connection for the corresponding thread.

Answer 11

Restart MySQL, it works fine.

BUT beware that if such a query is stuck, there is a problem somewhere :

• in your query (misplaced char, cartesian product, ...)
• very numerous records to edit
• complex joins or tests (MD5, substrings, LIKE %...%, etc.)
• data structure problem
• foreign key model (chain/loop locking)
• misindexed data

As @syedrakib said, it works but this is no long-living solution for production.

Beware : doing the restart can affect your data with inconsistent state.

Also, you can check how MySQL handles your query with the EXPLAIN keyword and see if something is possible there to speed up the query (indexes, complex tests,...).

Answer 12

I had this problem when trying to delete a certain group of records (using MS Access 2007 with an ODBC connection to MySQL on a web server). Typically I would delete certain records from MySQL then replace with updated records (cascade delete several related records, this streamlines deleting all related records for a single record deletion).

I tried to run through the operations available in phpMyAdmin for the table (optimize,flush, etc), but I was getting a need permission to RELOAD error when I tried to flush. Since my database is on a web server, I couldn't restart the database. Restoring from a backup was not an option.

I tried running delete query for this group of records on the cPanel mySQL access on the web. Got same error message.

My solution: I used Sun's (Oracle's) free MySQL Query Browser (that I previously installed on my computer) and ran the delete query there. It worked right away, Problem solved. I was then able to once again perform the function using the Access script using the ODBC Access to MySQL connection.

Answer 13

I had the same issue. I think it was a deadlock issue with SQL. You can just force close the SQL process from Task Manager. If that didn't fix it, just restart your computer. You don't need to drop the table and reload the data.

Answer 14

I ran into the same problem with an "update"-statement. My solution was simply to run through the operations available in phpMyAdmin for the table. I optimized, flushed and defragmented the table (not in that order). No need to drop the table and restore it from backup for me. :)