What happened to deep db?

When I was at Percona Live last year, there seemed to be a lot of excitement around what DeepDB could do for MySQL users. Their sales people kept hounding me to try it out but I didn't have time. I saw some news articles that they have open sourced the technology and now are being called Deep Software Foundation (http://www.deepis.org).

They had a lot of good blog posts and I really want to see how this technology progresses. Here are some interesting blog posts:

http://dev.deepis.com.473elmp01.blackmesh.com/blog/innodb-writing-challenges
http://dev.deepis.com.473elmp01.blackmesh.com/insights/blog/understanding-science-databases
http://dev.deepis.com.473elmp01.blackmesh.com/insights/blog/reimaging-science-databases
http://dev.deepis.com.473elmp01.blackmesh.com/blog/mysql-keep-grumbling

References to news articles:

https://finance.yahoo.com/news/deep-information-sciences-goes-open-130000559.html

https://www.businesswire.com/news/home/20170502005138/en/Deep-Information-Sciences-Open-Source-Relaunches-Deep

Disabling selinux on CentOS

If you try to run MySQL with selinux running on CentOS, you will get vague permission denied error like the following. It is frustaring to figure out why MySQL will not start because it does not point to SElinux being the problem.

/usr/sbin/mysqld: Can't find file: './mysql/plugin.frm' (errno: 13 - Permission denied)
2017-04-20 21:01:43 20164 [ERROR] Can't open the mysql.plugin table. Please run mysql_upgrade to create

Starting MySQL (Percona Server). ERROR! The server quit without updating PID file


rm: cannot remove `/var/lib/mysql/SERVERNAME.pid': Permission denied
 ERROR! The server quit without updating PID file (/var/lib/SERVERNAME.pid).

Check your log file to see what errors MySQL is generating during the start up process.

You can turn it off like this:

echo 0 >/selinux/enforce

Credit to:

https://www.cyberciti.biz/faq/howto-turn-off-selinux/

More things to know about events in MySQL

Events in MySQL are very useful for having some action kick off on a regular basis. I've used them for adding/removing partitions, killing long running queries and archiving data. However, when working with replication, they can some times be tricky. The data charmer wrote a blog post a few years ago which is useful:

http://datacharmer.blogspot.com/2009/03/something-to-know-about-event-scheduler.html

This is also a good reference:
http://anothermysqldba.blogspot.com/2013/05/using-mysql-event-scheduler.html

In MySQL only the master has running events. The event itself is replicated to the slave but is "SLAVESIDE_DISABLED". The tricky part is when you want to promote a slave to be a master. The event does not become ENABLED until you run an alter command like this:

ALTER EVENT <schema_name>.<event_name> ENABLE;

Also turning on the event scheduler does not enable individual events.

Your failover process could include a script that checks the slave for all events that are SLAVESIDE_DISABLED and then changes them to ENABLE when promoting a slave to a master. One of the tricky parts I have also experienced is when adding a new slave-replica to a cluster. I would copy over a previous backup from XtraBackup and then my script would add the slave into the cluster. If the backup contained events all the events on the SLAVE would be ENABLED. If the event was doing some thing like adding or removing partitions then I would notice that replication would break because the slave was doing what the master was also doing and when the statements were replicated to the slave, they would fail. I needed to add a check to my script which adds new slaves to a cluster and make all the events SLAVESIDE_DISABLED by running this on each event on the new replica:

ALTER EVENT zabbix.RotatePartitionedTables disable on slave;

Last_IO_Error: Got fatal error 1236 from master when reading data from binary log: 'Could not find first log file name in binary log index file'

Today I was trying to restore a backup onto a server and then add that new server into a replication cluster. I have a script that automatically does this by capturing the binary log position and log file that the slave should use when attaching to the master. Then the slave can use the binary log and relay file to catch up.

Each time I attempted this I would get this error:

Last_IO_Error: Got fatal error 1236 from master when reading data from binary log: 'Could not find first log file name in binary log index file'

I was wondering, who the heck keeps purging the binary logs before my new slave has time to replicate the data?

I checked the my.cnf file for the master and the logs are set to expire after 14 days. I was using a backup taken from this morning.

I checked the root's crontab and there was a little bash script running every hour doing this:

#!/bin/bash
time_string=$(date +"%Y-%m-%d %H:%M:%S" -d  "1 hour ago"); mysql -uUSERNAME --password=PASSWORD -e "purge binary logs before '${time_string}'"

That little bash script is purging all the binary logs from an hour before it starts so my script wasn't able to attach to the master and replicate because the log file which my backup was referencing files that had already been purged.

This is an extremely busy server that generates a lot of logs so I can see why this was here.

I temporary commented out the entry, started a new backup and finished adding my new slave into the server.

I also added an FYI to /etc/motd so that when someone logs in to the serverr via SSH they get a message indicating that this cron job is running.

pt-deadlock-logger

There are a number of options to run the deadlock logging tool but there is an actual example:

pt-deadlock-logger h=my_logging_server.com --user=USERNAME --password=PASSWORD --dest h=my_server.com,D=percona_schema,t=deadlocks,u=USERNAME,p=PASSWORD --create-dest-table --daemonize

This is the most useful free way I've found to capture deadlocks in MySQL.

Yet another meaningless MySQL error: Incorrect key file for table

I was running a data collection query against all the MySQL servers for a client and I kept getting an error with a message like this: "Incorrect key file for table '/tmp/#sql_4d51_0.MYI'; try to repair it"

I was thinking...what? That is entirely meaningless to me. Initially, I wasn't even sure what was causing that error. Every time I gather data from a server, I import it to different server for safe keeping. I thought it was the import process that had "incorrect key". After some troubleshooting, I narrowed it down to a single server which I was running the query on.

I found this answer here: http://stackoverflow.com/questions/11805793/incorrect-key-file-for-table-tmp-sql-3c51-0-myi-try-to-repair-it

However, the accepted answer was wrong for my case. The next answer was more correct but still not exactly what had happened. I logged onto the server and /tmp wasn't full. The data drive where the MySQL data files are stored was full! I don't know why but this particular server was not alerting in the monitoring system but I happened to find this problem indirectly by trying to run a query on the MySQL instance.

I wish that MySQL error like this were more clear about what are some of the potential causes of this error message.

GET_LOCK problem

I saw an interesting problem with the use of MySQL's GET_LOCK today. A client sent a notification that they are getting a lot of the following type of errors:

DAEMON: job=importFILE; exception=System.Exception: GET_LOCK failed: 0 

I logged onto the database that was having the problems and at any given time, I see about 5 or 6 running connections with this:

SELECT GET_LOCK('MyTableLock',10)

The application was running code like this:

                @"START TRANSACTION;

                SELECT GET_LOCK('MyTableLock',10);

                INSERT INTO MyTable (id, customer_id, process_id, value) VALUES (-1,-1,null,'-');

                INSERT INTO MyTable (id, customer_id, process_id, value) SELECT -1, -1,(LAST_INSERT_ID() + @vnum - 1) + 20, '-' from MyTable limit 1;

                SELECT LAST_INSERT_ID() + 20;

                SELECT RELEASE_LOCK('MyTableLock');

                ROLLBACK;";

It appeared the code would issue a GET_LOCK which would be followed by an error before the RELEASE_LOCK happened. The error didn’t cause the session to terminate and it was released back into the pool with the lock still held.  

The code didn't reset sessions so the next connection from the connection pool would still have that lock held. At this point, there would no longer be anything running that would have needed that lock. 

For a work around, we restarted the application process and killed the sessions that were running the GET_LOCK. Ultimately the code needs to be re-written to take this into account.

Here is some reading on what GET_LOCK does:
http://techblog.procurios.nl/k/news/view/41405/14863/mysql-get_lock()-explained.html
https://dev.mysql.com/doc/refman/5.7/en/miscellaneous-functions.html