Over the years you collect datasets you have created for various types of testing, seeding databases etc. I have always thought one needs to better manage this for future re-use. Recently I wanted to do some “Big Data” playing and again that question of what datasets can I use let me to review the past collated list at Seeking public data for benchmarks.

The types of things I was wanting to do lead me to realize a lot of content is “public domain” and Project Gutenberg is just one great source of text in multiple languages. This was just one aspect of my wish list but text based data is used from blogs, comments, articles, microblogs etc, and multiple languages was important from some text analysis.

With a bit of thinking about the building blocks, I created Good Test Data. A way for me to have core data, IP’s, people’s names, User Agents strings, text for articles, comments and a lot more. And importantly the ability to generate large randomized amounts of this data quickly and easily.

Now I can build a list of 1 million random names with unique usernames and emails with ease. I can generate millions of varying articles, from a short microblog, a comment, a blog to a multi page article. Then be able to produce HTML/PDF/PNG versions giving me file attachments. I’ve been playing more with image generation, creating banner images with varying text, and now I’m generating MP4 video to simulate the various standard sizes for advertising and just to see what people need.

I’m not sure of the potential use and benefit for others and that wasn’t the primary goal, however I would like to know how these building blocks could be used. The data is relatively agnostic, being able to easily load into MySQL tables. Depending on demand, being able to create pre-configured open source product data for e-commence products, CRM or blogging are all possible options.

It is common practice to grant your application the privileges of “GRANT SELECT, INSERT, UPDATE, DELETE ON yourdb.* TO user@host”.

But what if you want to ensure you cannot DELETE data from just one table?

Ideally I want to be able to “REVOKE DELETE ON yourdb.important_table FROM user@host”. You cannot do currently this with the MySQL privilege system.

If your schema has 100 tables, and you want to remove DELETE from one, you have to define DELETE for the 99 others, and remember that for each new table, you need to remember to also modify user privileges.

I recently came across an issue trying to connect to a MySQL server using the mysql client. It appeared as through the connection was hanging.

A subsequent connection using the -A option highlighted the problem with the previous connection stuck in the state “Waiting for table metadata lock”.

mysql> SHOW PROCESSLISTG
*************************** 1. row ***************************
     Id: 37
   User: root
   Host: localhost
     db: tmp
Command: Query
   Time: 90
  State: preparing
   Info: create table missing as select id from AK where id not in (select id ..
*************************** 2. row ***************************
     Id: 38
   User: root
   Host: localhost
     db: tmp
Command: Field List
   Time: 50
  State: Waiting for table metadata lock
   Info:
*************************** 3. row ***************************
     Id: 39
   User: root
   Host: localhost
     db: tmp
Command: Query
   Time: 0
  State: init
   Info: show processlist

In this example you can see a long running CREATE TABLE … SELECT statement as the cause of the problem. The -A or –no-auto-rehash argument is a means of disabling the tab completion in the mysql command line client.

Next week the US celebrates Thanksgiving Day. For those that are American or live here, this is a significant event. Three different experiences recently have lead me to write this request for ALL MySQL community members to give thanks to those that have contributed to the MySQL ecosystem. I have made a commitment to myself, and I would like to challenge others to write one book review per week in December, that’s 4 book reviews to the MySQL books that I have on my bookshelf that have made an impact in some way. I ask others to give it a go too.

It only takes a few minutes to pen a comment on Amazon, or a publishers site, but to authors it means so much more. I can only speak for myself, but any comment; good, bad or ugly; helps to know you are out there and you took the time to acknowledge somebody’s work of art (in this case a publication).

I only have to look at my bookshelf and I find the following MySQL books (in order they currently are placed which is no specific order), MySQL Crash Course by Ben Forta, MySQL Clustering by Alex Davies and Harrison Fisk, MySQL Cookbook by Paul DuBois, MySQL Stored Procedure Programming by Guy Harrison, Developing Web Applications with Apache, MySQL, memcached, and Perl by Patrick Galbraith, Pro MySQL (The Expert’s Voice in Open Source) by Mike Kruckenberg and Jay Pipes, MySQL Administrator’s Bible by Sheeri Cabral, MySQL (Third Edition) by Paul DuBois, High Performance MySQL: Optimization, Backups, Replication, and More (Second Edition) by Baron Schwartz, Peter Zaitsev, Vadim Tkachenko, Jeremy Zawodny, Arjen Lentz and Derek Balling, High Performance MySQL: Optimization, Backups, and Replication (Third Edition) by Baron Schwartz, Peter Zaitsev, Vadim Tkachenkoo, MySQL High Availability: Tools for Building Robust Data Centers by Charles Bell, Mats Kindal and Lars Thalman, Expert PHP and MySQLby Andrew Curiso, Ronald Bradford and Patrick Galbraith, Effective MySQL Backup and Recovery (Oracle Press) by Ronald Bradford, Effective MySQL Replication Techniques in Depth by Ronald Bradford and Chris Schneider, Effective MySQL Optimizing SQL Statements (Oracle Press) by Ronald Bradford, Database in Depth: Relational Theory for Practitioners by Chris Date, Pentaho Solutions: Business Intelligence and Data Warehousing with Pentaho and MySQL by Roland Bouman and Josh an Dongen, MySQL Administrator’s Guide and Language Reference (2nd Edition) and MySQL 5.0 Certification Study Guide by Paul Dubois, Stefan Hinz and Cartsten Pedersen.

And they are just the physical books, I have several PDF and Kindle only versions, and other MySQL Books I know about and have not purchased.

I would also like to give a special shout out to Sheeri Cabral and MySQL Marinate. A program using the O’Reilly Learning MySQL book to help anybody that wants to learn. At my most recent Effective MySQL Meetup a beginner question was asked by an audience member, and it was another audience member (not even myself) that piped up and recommended MySQL Marinate.

Finally, I learned MySQL by reading the online reference manual from cover to cover, and I did it again several years later, and probably should do it again some day. I am unable to find the names of the authors present or past, nor the right place you could leave a comment, but thanks to those I do know about, Jon Stephens, Mike Hillyer, Stefan Hinz, MC Brown and Paul DuBois.

Translating theory to practice is never easy. Morgan gives us the right steps in a play environment to move from dev.mysql.com native MySQL rpm’s to the new MySQL yum repository. I thought I would try it out.

1. Confirming existing packages

A necessary step, however immediately I have more dependencies including Perl DBD (used in several utilities) including MHA.

$ sudo su -
$ rpm -qa | grep -i mysql
MySQL-devel-5.6.13-1.el6.x86_64
MySQL-test-5.6.13-1.el6.x86_64
MySQL-shared-compat-5.6.13-1.el6.x86_64
MySQL-server-5.6.13-1.el6.x86_64
perl-DBD-MySQL-4.013-3.el6.x86_64
MySQL-client-5.6.13-1.el6.x86_64
MySQL-embedded-5.6.13-1.el6.x86_64
MySQL-shared-5.6.13-1.el6.x86_64
mha4mysql-node-0.54-1.el5.noarch

A further trap in the more complex real-world environments, in my case the installation of Percona XtraBackup. This will become apparent in the next step. We need to check for these packages.

$ rpm -qa | grep -i percona
percona-release-0.0-1.x86_64
percona-xtrabackup-2.1.4-656.rhel6.x86_64

1. Update your environment

There is a mixed blessing here. Assuming you keep your machines current (and you should), the impact here should be minimal, but buyer beware. In my case the update wanted to update java-1.7.0-openjdk. Should not be a big deal, but what other products are impacted by updates? Java on this system for example is used by the New Relic MySQL Monitoring. What if there was some important application component that may become unravelled with some update.

Doing a blanket update on a reasonably current CentOS 6.4 system broke.

$ yum update
...
Installing:
 Percona-SQL-shared-compat                      x86_64                5.0.92-b23.89.rhel6                      percona                1.1 M
     replacing  MySQL-shared.x86_64 5.6.13-1.el6
 Percona-Server-shared-compat                   x86_64                5.5.34-rel32.0.591.rhel6                 percona                3.4 M
     replacing  MySQL-shared.x86_64 5.6.13-1.el6
 Percona-Server-shared-compat-51                x86_64                5.1.72-rel14.10.597.rhel6                percona                2.4 M
     replacing  MySQL-shared.x86_64 5.6.13-1.el6
 kernel                                         x86_64                2.6.32-358.23.2.el6                      updates                 26 M
Transaction Summary
============================================================================================================================================
Install       4 Package(s)
Upgrade      26 Package(s)

...
Transaction Check Error:
  file /usr/lib64/libmysqlclient.so.12.0.0 from install of Percona-SQL-shared-compat-5.0.92-b23.89.rhel6.x86_64 conflicts with file from package MySQL-shared-compat-5.6.13-1.el6.x86_64
  file /usr/lib64/libmysqlclient.so.14.0.0 from install of Percona-SQL-shared-compat-5.0.92-b23.89.rhel6.x86_64 conflicts with file from package MySQL-shared-compat-5.6.13-1.el6.x86_64
  file /usr/lib64/libmysqlclient_r.so.12.0.0 from install of Percona-SQL-shared-compat-5.0.92-b23.89.rhel6.x86_64 conflicts with file from package MySQL-shared-compat-5.6.13-1.el6.x86_64
  file /usr/lib64/libmysqlclient_r.so.14.0.0 from install of Percona-SQL-shared-compat-5.0.92-b23.89.rhel6.x86_64 conflicts with file from package MySQL-shared-compat-5.6.13-1.el6.x86_64
  file /usr/lib64/libmysqlclient.so.16.0.0 from install of Percona-Server-shared-compat-5.5.34-rel32.0.591.rhel6.x86_64 conflicts with file from package MySQL-shared-compat-5.6.13-1.el6.x86_64
  file /usr/lib64/libmysqlclient_r.so.16.0.0 from install of Percona-Server-shared-compat-5.5.34-rel32.0.591.rhel6.x86_64 conflicts with file from package MySQL-shared-compat-5.6.13-1.el6.x86_64
  file /usr/lib64/libmysqlclient.so.12.0.0 conflicts between attempted installs of Percona-Server-shared-compat-5.5.34-rel32.0.591.rhel6.x86_64 and Percona-SQL-shared-compat-5.0.92-b23.89.rhel6.x86_64
  file /usr/lib64/libmysqlclient.so.14.0.0 conflicts between attempted installs of Percona-Server-shared-compat-5.5.34-rel32.0.591.rhel6.x86_64 and Percona-SQL-shared-compat-5.0.92-b23.89.rhel6.x86_64
  file /usr/lib64/libmysqlclient_r.so.12.0.0 conflicts between attempted installs of Percona-Server-shared-compat-5.5.34-rel32.0.591.rhel6.x86_64 and Percona-SQL-shared-compat-5.0.92-b23.89.rhel6.x86_64
  file /usr/lib64/libmysqlclient_r.so.14.0.0 conflicts between attempted installs of Percona-Server-shared-compat-5.5.34-rel32.0.591.rhel6.x86_64 and Percona-SQL-shared-compat-5.0.92-b23.89.rhel6.x86_64
...

The problem here is an unhealthy relationship between repositories for Percona Xtrabackup. I don’t know the reason, but this is the curse of dependencies that make real world upgrades more complex.

Updating just MySQL is rather useless as it’s installed by rpm.

$ yum update MySQL-server
Loaded plugins: fastestmirror, presto
Loading mirror speeds from cached hostfile
 * base: mirror.cogentco.com
 * extras: mirror.cogentco.com
 * updates: mirror.trouble-free.net
Setting up Update Process
No Packages marked for Update

Removing existing MySQL

Stopping MySQL is easy. Making a decision about, should I backup important files, like the config file, or the data should be considered here. The reality is for a production system, assume something unexpected will happen, even if you have tested it. Being able to go back in any step of an upgrade is actually more important than the step itself. So the following IS NOT ENOUGH in a production system.

service mysql stop

This old dinosaur learned a new trick in the yum interactive shell. Cool!

Note, I am doing a point release upgrade here, from .13 to .14.

$ yum shell
> remove MySQL-client-5.6.13-1.el6 MySQL-embedded-5.6.13-1.el6 MySQL-server-5.6.13-1.el6 MySQL-shared-5.6.13-1.el6 MySQL-devel-5.6.13-1.el6 MySQL-test-5.6.13-1.el6 MySQL-shared-compat-5.6.13-1.el6
> install mysql-community-server
> run

Now the fun begins, you have to read carefully what is happening, check out the Removing for dependencies section.

============================================================================================================================================
 Package                              Arch                 Version                            Repository                               Size
============================================================================================================================================
Installing:
 mysql-community-server               x86_64               5.6.14-3.el6                       mysql-community                          51 M
Removing:
 MySQL-client                         x86_64               5.6.13-1.el6                       installed                                81 M
 MySQL-devel                          x86_64               5.6.13-1.el6                       installed                                19 M
 MySQL-embedded                       x86_64               5.6.13-1.el6                       installed                               431 M
 MySQL-server                         x86_64               5.6.13-1.el6                       installed                               235 M
 MySQL-shared                         x86_64               5.6.13-1.el6                       installed                               8.4 M
 MySQL-shared-compat                  x86_64               5.6.13-1.el6                       installed                                11 M
 MySQL-test                           x86_64               5.6.13-1.el6                       installed                               318 M
Installing for dependencies:
 mysql-community-client               x86_64               5.6.14-3.el6                       mysql-community                          18 M
 mysql-community-common               x86_64               5.6.14-3.el6                       mysql-community                         296 k
 mysql-community-libs                 x86_64               5.6.14-3.el6                       mysql-community                         1.8 M
Removing for dependencies:
 cronie                               x86_64               1.4.4-7.el6                        @CentOS6-Base/$releasever               166 k
 cronie-anacron                       x86_64               1.4.4-7.el6                        @CentOS6-Base/$releasever                43 k
 crontabs                             noarch               1.10-33.el6                        @CentOS6-Base/$releasever               2.4 k
 mha4mysql-node                       noarch               0.54-1.el5                         installed                                98 k
 percona-xtrabackup                   x86_64               2.1.4-656.rhel6                    @percona                                 24 M
 perl-DBD-MySQL                       x86_64               4.013-3.el6                        @base                                   338 k
 postfix                              x86_64               2:2.6.6-2.2.el6_1                  @CentOS6-Base/$releasever               9.7 M
 sysstat                              x86_64               9.0.4-20.el6                       @base                                   807 k

Transaction Summary
============================================================================================================================================
Install       4 Package(s)
Remove       15 Package(s)

Also, you need to quit the yum shell.

> quit
Leaving Shell

Verification

So, we have now installed MySQL via the new yum repositories, and we can verify this.

$ service mysqld start
Starting mysqld:                                           [  OK  ]
$ mysql -e "SELECT VERSION()"
+------------+
| VERSION()  |
+------------+
| 5.6.14-log |
+------------+
$ chkconfig mysqld on

But, we now have a broken system, because dependencies were removed.

Extra steps needed

Installation of Percona Backup.

$ yum install percona-xtrabackup
Loaded plugins: fastestmirror, presto
Loading mirror speeds from cached hostfile
 * base: mirrors.advancedhosters.com
 * extras: mirror.cogentco.com
 * updates: mirror.trouble-free.net
Setting up Install Process
Resolving Dependencies
--> Running transaction check
---> Package percona-xtrabackup.x86_64 0:2.1.5-680.rhel6 will be installed
--> Processing Dependency: perl(DBD::mysql) for package: percona-xtrabackup-2.1.5-680.rhel6.x86_64
--> Running transaction check
---> Package perl-DBD-MySQL.x86_64 0:4.013-3.el6 will be installed
--> Processing Dependency: libmysqlclient.so.16(libmysqlclient_16)(64bit) for package: perl-DBD-MySQL-4.013-3.el6.x86_64
--> Processing Dependency: libmysqlclient.so.16()(64bit) for package: perl-DBD-MySQL-4.013-3.el6.x86_64
--> Running transaction check
---> Package Percona-Server-shared-51.x86_64 0:5.1.72-rel14.10.597.rhel6 will be installed
--> Finished Dependency Resolution

Dependencies Resolved

============================================================================================================================================
 Package                                  Arch                   Version                                      Repository               Size
============================================================================================================================================
Installing:
 percona-xtrabackup                       x86_64                 2.1.5-680.rhel6                              percona                 6.8 M
Installing for dependencies:
 Percona-Server-shared-51                 x86_64                 5.1.72-rel14.10.597.rhel6                    percona                 2.1 M
 perl-DBD-MySQL                           x86_64                 4.013-3.el6                                  base                    134 k

Transaction Summary
============================================================================================================================================
Install       3 Package(s)

Total size: 9.1 M
Total download size: 2.3 M
Installed size: 30 M
Is this ok [y/N]: y
Downloading Packages:
Setting up and reading Presto delta metadata
Processing delta metadata
Package(s) data still to download: 2.3 M
(1/2): Percona-Server-shared-51-5.1.72-rel14.10.597.rhel6.x86_64.rpm                                                 | 2.1 MB     00:00
(2/2): perl-DBD-MySQL-4.013-3.el6.x86_64.rpm                                                                         | 134 kB     00:00
--------------------------------------------------------------------------------------------------------------------------------------------
Total                                                                                                       9.7 MB/s | 2.3 MB     00:00
Running rpm_check_debug
Running Transaction Test
Transaction Test Succeeded
Running Transaction
  Installing : Percona-Server-shared-51-5.1.72-rel14.10.597.rhel6.x86_64                                                                1/3
  Installing : perl-DBD-MySQL-4.013-3.el6.x86_64                                                                                        2/3
  Installing : percona-xtrabackup-2.1.5-680.rhel6.x86_64                                                                                3/3
  Verifying  : percona-xtrabackup-2.1.5-680.rhel6.x86_64                                                                                1/3
  Verifying  : perl-DBD-MySQL-4.013-3.el6.x86_64                                                                                        2/3
  Verifying  : Percona-Server-shared-51-5.1.72-rel14.10.597.rhel6.x86_64                                                                3/3

Installed:
  percona-xtrabackup.x86_64 0:2.1.5-680.rhel6

Dependency Installed:
  Percona-Server-shared-51.x86_64 0:5.1.72-rel14.10.597.rhel6                      perl-DBD-MySQL.x86_64 0:4.013-3.el6

Complete!

Please explain this one to be batman, removing MySQL removed the sysstat package. Very weird.

$ iostat
-bash: iostat: command not found
$ yum install sysstat
Loaded plugins: fastestmirror, presto
Loading mirror speeds from cached hostfile
 * base: mirrors.advancedhosters.com
 * extras: mirror.cogentco.com
 * updates: centos.someimage.com
Setting up Install Process
Resolving Dependencies
--> Running transaction check
---> Package sysstat.x86_64 0:9.0.4-20.el6 will be installed
--> Processing Dependency: /etc/cron.d for package: sysstat-9.0.4-20.el6.x86_64
--> Running transaction check
---> Package cronie.x86_64 0:1.4.4-7.el6 will be installed
--> Processing Dependency: dailyjobs for package: cronie-1.4.4-7.el6.x86_64
--> Processing Dependency: /usr/sbin/sendmail for package: cronie-1.4.4-7.el6.x86_64
--> Running transaction check
---> Package cronie-anacron.x86_64 0:1.4.4-7.el6 will be installed
--> Processing Dependency: crontabs for package: cronie-anacron-1.4.4-7.el6.x86_64
---> Package postfix.x86_64 2:2.6.6-2.2.el6_1 will be installed
--> Running transaction check
---> Package crontabs.noarch 0:1.10-33.el6 will be installed
--> Finished Dependency Resolution

Dependencies Resolved

============================================================================================================================================
 Package                              Arch                         Version                                 Repository                  Size
============================================================================================================================================
Installing:
 sysstat                              x86_64                       9.0.4-20.el6                            base                       225 k
Installing for dependencies:
 cronie                               x86_64                       1.4.4-7.el6                             base                        70 k
 cronie-anacron                       x86_64                       1.4.4-7.el6                             base                        29 k
 crontabs                             noarch                       1.10-33.el6                             base                        10 k
 postfix                              x86_64                       2:2.6.6-2.2.el6_1                       base                       2.0 M

Transaction Summary
============================================================================================================================================
Install       5 Package(s)

Total download size: 2.4 M
Installed size: 11 M
Is this ok [y/N]: y
Downloading Packages:
Setting up and reading Presto delta metadata
Processing delta metadata
Package(s) data still to download: 2.4 M
(1/5): cronie-1.4.4-7.el6.x86_64.rpm                                                                                 |  70 kB     00:00
(2/5): cronie-anacron-1.4.4-7.el6.x86_64.rpm                                                                         |  29 kB     00:00
(3/5): crontabs-1.10-33.el6.noarch.rpm                                                                               |  10 kB     00:00
(4/5): postfix-2.6.6-2.2.el6_1.x86_64.rpm                                                                            | 2.0 MB     00:00
(5/5): sysstat-9.0.4-20.el6.x86_64.rpm                                                                               | 225 kB     00:00
--------------------------------------------------------------------------------------------------------------------------------------------
Total                                                                                                        21 MB/s | 2.4 MB     00:00
Running rpm_check_debug
Running Transaction Test
Transaction Test Succeeded
Running Transaction
  Installing : 2:postfix-2.6.6-2.2.el6_1.x86_64                                                                                         1/5
  Installing : cronie-1.4.4-7.el6.x86_64                                                                                                2/5
  Installing : crontabs-1.10-33.el6.noarch                                                                                              3/5
  Installing : cronie-anacron-1.4.4-7.el6.x86_64                                                                                        4/5
  Installing : sysstat-9.0.4-20.el6.x86_64                                                                                              5/5
  Verifying  : crontabs-1.10-33.el6.noarch                                                                                              1/5
  Verifying  : cronie-1.4.4-7.el6.x86_64                                                                                                2/5
  Verifying  : 2:postfix-2.6.6-2.2.el6_1.x86_64                                                                                         3/5
  Verifying  : sysstat-9.0.4-20.el6.x86_64                                                                                              4/5
  Verifying  : cronie-anacron-1.4.4-7.el6.x86_64                                                                                        5/5

Installed:
  sysstat.x86_64 0:9.0.4-20.el6

Dependency Installed:
  cronie.x86_64 0:1.4.4-7.el6    cronie-anacron.x86_64 0:1.4.4-7.el6    crontabs.noarch 0:1.10-33.el6    postfix.x86_64 2:2.6.6-2.2.el6_1

Complete!

Re-installing MySQL MHA node.

$ cd /tmp
$ wget http://mysql-master-ha.googlecode.com/files/mha4mysql-node-0.54-0.el6.noarch.rpm
$ sudo rpm -ivh mha4mysql-node-*.noarch.rpm

There is now a lot more work needed to check and recheck the dependencies and verify what did work previously still works.

At this time doing this on 20 DB servers to move to the new yum repository is a fail for this client. It’s simply not worth it.

Conclusion

Theory easy, practice not to easy!

Recently a client asked me how long it would take for an ALTER TABLE to complete. Generally the answer is “it depends”. While this was running on a production system I tried with the Performance Schema in MySQL 5.6 to work out some answer to this question. While I never got to investigate various tests using INPLACE and COPY for comparison, Morgan Tocker made the request for experiences with online ALTER in A closer look at Online DDL in MySQL 5.6. Hopefully somebody with more time can expand on my preliminary observations.

Using Mark Leith’s ps_helper (older version) I monitored the File I/O to see if I could determine when using innodb_file_per_table the percentage of table writing to be completed.

Other data access on this slave server was disabled, so these results represent the I/O of a single ALTER TABLE statement.

• We can clearly see the reading of the Txxxxxxxxxxxxxx.ibd table,starting at 4.03G, then 7.79G, and following that a peak of 9.75 GB.
• We see the writing of Txxxxxxxxxxxxxx.ibd in the last samples, and it completes 9.85 GB, the “write_pct” is shows ~50%, a good indicator of a total read and write of the table
• What we also see is an “Innodb Merge Temp File” which is initially all writes, an indication of what may be a “copy”, however what is *interesting* is the amount of reads and writes are 6X the size of the underlying table
• Recall that this server is effectively *idle*, so there is no need to be keeping version information of actual table changes
• This “Innodb Merge Temp File” also works in 1MB chunks, so comparing the “count” values between the base table of 16K operations can be misleading if you just look at count deltas during the process.

Given more time, I would have performed more extensive monitoring including timestamps, and run a test using the COPY algorithm to see if this took less time.

Sample 1

mysql> select * from ps_helper.io_global_by_file_by_bytes limit 10;
+---------------------------------------------+------------+------------+-----------+-------------+---------------+-----------+-----------+-----------+
| file                                        | count_read | total_read | avg_read  | count_write | total_written | avg_write | total     | write_pct |
+---------------------------------------------+------------+------------+-----------+-------------+---------------+-----------+-----------+-----------+
| @@datadir/nsikeyword/Txxxxxxxxxxxxxx.ibd    |     264207 | 4.03 GiB   | 16.00 KiB |         191 | 2.98 MiB      | 16.00 KiB | 4.03 GiB  |      0.07 |
| @@datadir/Innodb Merge Temp File            |          0 | 0 bytes    | 0 bytes   |        1912 | 1.87 GiB      | 1.00 MiB  | 1.87 GiB  |    100.00 |
| @@datadir/ibdata1                           |        412 | 8.41 MiB   | 20.89 KiB |         693 | 46.52 MiB     | 68.73 KiB | 54.92 MiB |     84.69 |
| @@datadir/ib_logfile1                       |          2 | 64.50 KiB  | 32.25 KiB |       16670 | 11.92 MiB     | 750 bytes | 11.98 MiB |     99.47 |
| /mysql/binlog/mysql-relay-bin.003236        |        749 | 5.85 MiB   | 8.00 KiB  |       49943 | 5.85 MiB      | 123 bytes | 11.70 MiB |     50.00 |
| @@datadir/mysql/slave_master_info.ibd       |          4 | 64.00 KiB  | 16.00 KiB |           0 | 0 bytes       | 0 bytes   | 64.00 KiB |      0.00 |
| @@datadir/mysql/slave_relay_log_info.ibd    |          4 | 64.00 KiB  | 16.00 KiB |           0 | 0 bytes       | 0 bytes   | 64.00 KiB |      0.00 |
| @@datadir/mysql/slave_worker_info.ibd       |          4 | 64.00 KiB  | 16.00 KiB |           0 | 0 bytes       | 0 bytes   | 64.00 KiB |      0.00 |
+---------------------------------------------+------------+------------+-----------+-------------+---------------+-----------+-----------+-----------+

Sample 2

mysql> select * from ps_helper.io_global_by_file_by_bytes limit 10;
+---------------------------------------------+------------+------------+-----------+-------------+---------------+-----------+-----------+-----------+
| file                                        | count_read | total_read | avg_read  | count_write | total_written | avg_write | total     | write_pct |
+---------------------------------------------+------------+------------+-----------+-------------+---------------+-----------+-----------+-----------+
| @@datadir/nsikeyword/Txxxxxxxxxxxxxx.ibd    |     510483 | 7.79 GiB   | 16.00 KiB |         191 | 2.98 MiB      | 16.00 KiB | 7.79 GiB  |      0.04 |
| @@datadir/Innodb Merge Temp File            |          0 | 0 bytes    | 0 bytes   |        3517 | 3.43 GiB      | 1.00 MiB  | 3.43 GiB  |    100.00 |
| @@datadir/ibdata1                           |        412 | 8.41 MiB   | 20.89 KiB |         693 | 46.52 MiB     | 68.73 KiB | 54.92 MiB |     84.69 |
| @@datadir/ib_logfile1                       |          2 | 64.50 KiB  | 32.25 KiB |       16670 | 11.92 MiB     | 750 bytes | 11.98 MiB |     99.47 |
| /mysql/binlog/mysql-relay-bin.003236        |        749 | 5.85 MiB   | 8.00 KiB  |       49943 | 5.85 MiB      | 123 bytes | 11.70 MiB |     50.00 |
| @@datadir/mysql/slave_master_info.ibd       |          4 | 64.00 KiB  | 16.00 KiB |           0 | 0 bytes       | 0 bytes   | 64.00 KiB |      0.00 |
| @@datadir/mysql/slave_relay_log_info.ibd    |          4 | 64.00 KiB  | 16.00 KiB |           0 | 0 bytes       | 0 bytes   | 64.00 KiB |      0.00 |
| @@datadir/mysql/slave_worker_info.ibd       |          4 | 64.00 KiB  | 16.00 KiB |           0 | 0 bytes       | 0 bytes   | 64.00 KiB |      0.00 |
+---------------------------------------------+------------+------------+-----------+-------------+---------------+-----------+-----------+-----------+

Sample 3

mysql> select * from ps_helper.io_global_by_file_by_bytes limit 10;
+---------------------------------------------+------------+------------+-----------+-------------+---------------+-----------+------------+-----------+
| file                                        | count_read | total_read | avg_read  | count_write | total_written | avg_write | total      | write_pct |
+---------------------------------------------+------------+------------+-----------+-------------+---------------+-----------+------------+-----------+
| @@datadir/Innodb Merge Temp File            |      19503 | 19.05 GiB  | 1.00 MiB  |       23798 | 23.24 GiB     | 1.00 MiB  | 42.29 GiB  |     54.96 |
| @@datadir/nsikeyword/Txxxxxxxxxxxxxx.ibd    |     638920 | 9.75 GiB   | 16.00 KiB |         191 | 2.98 MiB      | 16.00 KiB | 9.75 GiB   |      0.03 |
| @@datadir/ibdata1                           |        412 | 8.41 MiB   | 20.89 KiB |         693 | 46.52 MiB     | 68.73 KiB | 54.92 MiB  |     84.69 |
| @@datadir/ib_logfile1                       |          2 | 64.50 KiB  | 32.25 KiB |       16670 | 11.92 MiB     | 750 bytes | 11.98 MiB  |     99.47 |
| /mysql/binlog/mysql-relay-bin.003236        |        749 | 5.85 MiB   | 8.00 KiB  |       49943 | 5.85 MiB      | 123 bytes | 11.70 MiB  |     50.00 |
| @@datadir/mysql/proc.MYD                    |        692 | 423.96 KiB | 627 bytes |           0 | 0 bytes       | 0 bytes   | 423.96 KiB |      0.00 |
| @@datadir/mysql/slave_master_info.ibd       |          4 | 64.00 KiB  | 16.00 KiB |           0 | 0 bytes       | 0 bytes   | 64.00 KiB  |      0.00 |
| @@datadir/mysql/slave_relay_log_info.ibd    |          4 | 64.00 KiB  | 16.00 KiB |           0 | 0 bytes       | 0 bytes   | 64.00 KiB  |      0.00 |
+---------------------------------------------+------------+------------+-----------+-------------+---------------+-----------+------------+-----------+

Sample 4

mysql> select * from ps_helper.io_global_by_file_by_bytes limit 10;
+---------------------------------------------+------------+------------+-----------+-------------+---------------+-----------+------------+-----------+
| file                                        | count_read | total_read | avg_read  | count_write | total_written | avg_write | total      | write_pct |
+---------------------------------------------+------------+------------+-----------+-------------+---------------+-----------+------------+-----------+
| @@datadir/Innodb Merge Temp File            |      36865 | 36.00 GiB  | 1.00 MiB  |       41160 | 40.20 GiB     | 1.00 MiB  | 76.20 GiB  |     52.75 |
| @@datadir/nsikeyword/Txxxxxxxxxxxxxx.ibd    |     638920 | 9.75 GiB   | 16.00 KiB |         191 | 2.98 MiB      | 16.00 KiB | 9.75 GiB   |      0.03 |
| @@datadir/ibdata1                           |        412 | 8.41 MiB   | 20.89 KiB |         693 | 46.52 MiB     | 68.73 KiB | 54.92 MiB  |     84.69 |
| @@datadir/ib_logfile1                       |          2 | 64.50 KiB  | 32.25 KiB |       16670 | 11.92 MiB     | 750 bytes | 11.98 MiB  |     99.47 |
| /mysql/binlog/mysql-relay-bin.003236        |        749 | 5.85 MiB   | 8.00 KiB  |       49943 | 5.85 MiB      | 123 bytes | 11.70 MiB  |     50.00 |
| @@datadir/mysql/proc.MYD                    |        692 | 423.96 KiB | 627 bytes |           0 | 0 bytes       | 0 bytes   | 423.96 KiB |      0.00 |
| @@datadir/mysql/slave_master_info.ibd       |          4 | 64.00 KiB  | 16.00 KiB |           0 | 0 bytes       | 0 bytes   | 64.00 KiB  |      0.00 |
| @@datadir/mysql/slave_relay_log_info.ibd    |          4 | 64.00 KiB  | 16.00 KiB |           0 | 0 bytes       | 0 bytes   | 64.00 KiB  |      0.00 |
+---------------------------------------------+------------+------------+-----------+-------------+---------------+-----------+------------+-----------+

Sample 5

mysql> select * from ps_helper.io_global_by_file_by_bytes limit 10;
+---------------------------------------------+------------+------------+-----------+-------------+---------------+------------+------------+-----------+
| file                                        | count_read | total_read | avg_read  | count_write | total_written | avg_write  | total      | write_pct |
+---------------------------------------------+------------+------------+-----------+-------------+---------------+------------+------------+-----------+
| @@datadir/Innodb Merge Temp File            |      57009 | 55.67 GiB  | 1.00 MiB  |       60144 | 58.73 GiB     | 1.00 MiB   | 114.41 GiB |     51.34 |
| @@datadir/nsikeyword/Txxxxxxxxxxxxxx.ibd    |     638922 | 9.75 GiB   | 16.00 KiB |       92839 | 2.56 GiB      | 28.88 KiB  | 12.31 GiB  |     20.78 |
| @@datadir/ibdata1                           |        412 | 8.41 MiB   | 20.89 KiB |        8081 | 1.44 GiB      | 186.98 KiB | 1.45 GiB   |     99.43 |
| @@datadir/ib_logfile0                       |          4 | 3.50 KiB   | 896 bytes |        4443 | 845.59 MiB    | 194.89 KiB | 845.60 MiB |    100.00 |
| @@datadir/ib_logfile1                       |          2 | 64.50 KiB  | 32.25 KiB |       19327 | 735.53 MiB    | 38.97 KiB  | 735.60 MiB |     99.99 |
| /mysql/binlog/mysql-relay-bin.003236        |        749 | 5.85 MiB   | 8.00 KiB  |       49943 | 5.85 MiB      | 123 bytes  | 11.70 MiB  |     50.00 |
| @@datadir/mysql/proc.MYD                    |        696 | 426.43 KiB | 627 bytes |           0 | 0 bytes       | 0 bytes    | 426.43 KiB |      0.00 |
| @@datadir/mysql/slave_master_info.ibd       |          4 | 64.00 KiB  | 16.00 KiB |           0 | 0 bytes       | 0 bytes    | 64.00 KiB  |      0.00 |
+---------------------------------------------+------------+------------+-----------+-------------+---------------+------------+------------+-----------+

Sample 6

mysql> select * from ps_helper.io_global_by_file_by_bytes limit 10;
+---------------------------------------------+------------+------------+-----------+-------------+---------------+------------+------------+-----------+
| file                                        | count_read | total_read | avg_read  | count_write | total_written | avg_write  | total      | write_pct |
+---------------------------------------------+------------+------------+-----------+-------------+---------------+------------+------------+-----------+
| @@datadir/Innodb Merge Temp File            |      60144 | 58.73 GiB  | 1.00 MiB  |       60144 | 58.73 GiB     | 1.00 MiB   | 117.47 GiB |     50.00 |
| @@datadir/nsikeyword/Txxxxxxxxxxxxxx.ibd    |     638922 | 9.75 GiB   | 16.00 KiB |      348927 | 9.85 GiB      | 29.61 KiB  | 19.60 GiB  |     50.27 |
| @@datadir/ibdata1                           |        427 | 8.64 MiB   | 20.72 KiB |       31941 | 5.30 GiB      | 173.84 KiB | 5.30 GiB   |     99.84 |
| @@datadir/ib_logfile0                       |          4 | 3.50 KiB   | 896 bytes |       15763 | 2.97 GiB      | 197.34 KiB | 2.97 GiB   |    100.00 |
| @@datadir/ib_logfile1                       |          2 | 64.50 KiB  | 32.25 KiB |       29864 | 2.72 GiB      | 95.62 KiB  | 2.72 GiB   |    100.00 |
| /mysql/binlog/mysql-relay-bin.003236        |        749 | 5.85 MiB   | 8.00 KiB  |       49943 | 5.85 MiB      | 123 bytes  | 11.70 MiB  |     50.00 |
| @@datadir/mysql/proc.MYD                    |        700 | 428.89 KiB | 627 bytes |           0 | 0 bytes       | 0 bytes    | 428.89 KiB |      0.00 |
| @@datadir/mysql/innodb_index_stats.ibd      |          5 | 80.00 KiB  | 16.00 KiB |           1 | 16.00 KiB     | 16.00 KiB  | 96.00 KiB  |     16.67 |
+---------------------------------------------+------------+------------+-----------+-------------+---------------+------------+------------+-----------+

Working with MySQL 5.6 under CentOS 6.4 I came across the following problem with MySQL reporting it did not shutdown successfully.

$ sudo su -
$ service mysql stop
Shutting down MySQL................................................................................................................................................................................................................................................................................................
.........................................................................................................................................................................................................................................................................................................
.........................................................................................................................................................................................................................................................................................................
................. ERROR!

However, you have to look into the problem in the all important MySQL Error Log where I found a different story.

$ tail -100 /mysql/log/error.log
...
2013-11-04 14:43:40 32351 [Note] Shutting down plugin 'INNODB_LOCK_WAITS'
2013-11-04 14:43:40 32351 [Note] Shutting down plugin 'INNODB_LOCKS'
2013-11-04 14:43:40 32351 [Note] Shutting down plugin 'INNODB_TRX'
2013-11-04 14:43:40 32351 [Note] Shutting down plugin 'InnoDB'
2013-11-04 14:43:40 32351 [Note] InnoDB: FTS optimize thread exiting.
2013-11-04 14:43:40 32351 [Note] InnoDB: Starting shutdown...
2013-11-04 14:44:41 32351 [Note] InnoDB: Waiting for page_cleaner to finish flushing of buffer pool
2013-11-04 14:45:41 32351 [Note] InnoDB: Waiting for page_cleaner to finish flushing of buffer pool
2013-11-04 14:46:41 32351 [Note] InnoDB: Waiting for page_cleaner to finish flushing of buffer pool
2013-11-04 14:47:41 32351 [Note] InnoDB: Waiting for page_cleaner to finish flushing of buffer pool
2013-11-04 14:48:41 32351 [Note] InnoDB: Waiting for page_cleaner to finish flushing of buffer pool
2013-11-04 14:49:41 32351 [Note] InnoDB: Waiting for page_cleaner to finish flushing of buffer pool
2013-11-04 14:50:42 32351 [Note] InnoDB: Waiting for page_cleaner to finish flushing of buffer pool
2013-11-04 14:51:42 32351 [Note] InnoDB: Waiting for page_cleaner to finish flushing of buffer pool
2013-11-04 14:52:42 32351 [Note] InnoDB: Waiting for page_cleaner to finish flushing of buffer pool
2013-11-04 14:53:42 32351 [Note] InnoDB: Waiting for page_cleaner to finish flushing of buffer pool
2013-11-04 14:54:42 32351 [Note] InnoDB: Waiting for page_cleaner to finish flushing of buffer pool
2013-11-04 14:55:42 32351 [Note] InnoDB: Waiting for page_cleaner to finish flushing of buffer pool
2013-11-04 14:56:43 32351 [Note] InnoDB: Waiting for page_cleaner to finish flushing of buffer pool
2013-11-04 14:57:43 32351 [Note] InnoDB: Waiting for page_cleaner to finish flushing of buffer pool
2013-11-04 14:58:43 32351 [Note] InnoDB: Waiting for page_cleaner to finish flushing of buffer pool
2013-11-04 14:59:43 32351 [Note] InnoDB: Waiting for page_cleaner to finish flushing of buffer pool
2013-11-04 15:00:43 32351 [Note] InnoDB: Waiting for page_cleaner to finish flushing of buffer pool
2013-11-04 15:01:43 32351 [Note] InnoDB: Waiting for page_cleaner to finish flushing of buffer pool
2013-11-04 15:02:01 32351 [Note] InnoDB: Shutdown completed; log sequence number 109188218872
2013-11-04 15:02:01 32351 [Note] Shutting down plugin 'MRG_MYISAM'
2013-11-04 15:02:01 32351 [Note] Shutting down plugin 'CSV'
2013-11-04 15:02:01 32351 [Note] Shutting down plugin 'MEMORY'
2013-11-04 15:02:01 32351 [Note] Shutting down plugin 'MyISAM'
2013-11-04 15:02:01 32351 [Note] Shutting down plugin 'sha256_password'
2013-11-04 15:02:01 32351 [Note] Shutting down plugin 'mysql_old_password'
2013-11-04 15:02:01 32351 [Note] Shutting down plugin 'mysql_native_password'
2013-11-04 15:02:01 32351 [Note] Shutting down plugin 'binlog'
2013-11-04 15:02:01 32351 [Note] /usr/sbin/mysqld: Shutdown complete

131104 15:02:01 mysqld_safe mysqld from pid file /var/run/mysqld/mysql.pid ended

The log indicates that the server is actually shutdown, an attempt to try again results in

$ service mysql stop
 ERROR! MySQL server PID file could not be found!

Doing some more investigation to pinpoint if the issue is “service” (i.e. “init.d”) related, I found that the command took suspiciously exactly 15 minutes (on several occasions) and MySQL was indeed not shutdown. For example:

$ sudo su -
$ time service mysql stop; tail /mysql/log/error.log
Shutting down MySQL................................................................................................................................................................................................................................................................................................
..........................................................................................................................................................................................................................................................................................................
..........................................................................................................................................................................................................................................................................................................
................ ERROR!

real	15m4.003s
user	0m0.561s
sys	0m2.194s
2013-11-06 16:50:37 19887 [Note] InnoDB: Waiting for page_cleaner to finish flushing of buffer pool
2013-11-06 16:51:38 19887 [Note] InnoDB: Waiting for page_cleaner to finish flushing of buffer pool
2013-11-06 16:52:38 19887 [Note] InnoDB: Waiting for page_cleaner to finish flushing of buffer pool
2013-11-06 16:53:38 19887 [Note] InnoDB: Waiting for page_cleaner to finish flushing of buffer pool
2013-11-06 16:54:38 19887 [Note] InnoDB: Waiting for page_cleaner to finish flushing of buffer pool
2013-11-06 16:55:38 19887 [Note] InnoDB: Waiting for page_cleaner to finish flushing of buffer pool
2013-11-06 16:56:39 19887 [Note] InnoDB: Waiting for page_cleaner to finish flushing of buffer pool
2013-11-06 16:57:39 19887 [Note] InnoDB: Waiting for page_cleaner to finish flushing of buffer pool
2013-11-06 16:58:39 19887 [Note] InnoDB: Waiting for page_cleaner to finish flushing of buffer pool
2013-11-06 16:59:39 19887 [Note] InnoDB: Waiting for page_cleaner to finish flushing of buffer pool

However, waiting it did indeed complete successfully.

tail -f /mysql/log/error.log
2013-11-06 16:51:38 19887 [Note] InnoDB: Waiting for page_cleaner to finish flushing of buffer pool
2013-11-06 16:52:38 19887 [Note] InnoDB: Waiting for page_cleaner to finish flushing of buffer pool
2013-11-06 16:53:38 19887 [Note] InnoDB: Waiting for page_cleaner to finish flushing of buffer pool
2013-11-06 16:54:38 19887 [Note] InnoDB: Waiting for page_cleaner to finish flushing of buffer pool
2013-11-06 16:55:38 19887 [Note] InnoDB: Waiting for page_cleaner to finish flushing of buffer pool
2013-11-06 16:56:39 19887 [Note] InnoDB: Waiting for page_cleaner to finish flushing of buffer pool
2013-11-06 16:57:39 19887 [Note] InnoDB: Waiting for page_cleaner to finish flushing of buffer pool
2013-11-06 16:58:39 19887 [Note] InnoDB: Waiting for page_cleaner to finish flushing of buffer pool
2013-11-06 16:59:39 19887 [Note] InnoDB: Waiting for page_cleaner to finish flushing of buffer pool
2013-11-06 17:00:39 19887 [Note] InnoDB: Waiting for page_cleaner to finish flushing of buffer pool
2013-11-06 17:01:39 19887 [Note] InnoDB: Waiting for page_cleaner to finish flushing of buffer pool
2013-11-06 17:02:40 19887 [Note] InnoDB: Waiting for page_cleaner to finish flushing of buffer pool
2013-11-06 17:03:03 19887 [Note] InnoDB: Shutdown completed; log sequence number 109974145720
2013-11-06 17:03:03 19887 [Note] Shutting down plugin 'MRG_MYISAM'
2013-11-06 17:03:03 19887 [Note] Shutting down plugin 'CSV'
2013-11-06 17:03:03 19887 [Note] Shutting down plugin 'MEMORY'
2013-11-06 17:03:03 19887 [Note] Shutting down plugin 'MyISAM'
2013-11-06 17:03:03 19887 [Note] Shutting down plugin 'sha256_password'
2013-11-06 17:03:03 19887 [Note] Shutting down plugin 'mysql_old_password'
2013-11-06 17:03:03 19887 [Note] Shutting down plugin 'mysql_native_password'
2013-11-06 17:03:03 19887 [Note] Shutting down plugin 'binlog'
2013-11-06 17:03:03 19887 [Note] /usr/sbin/mysqld: Shutdown complete

131106 17:03:03 mysqld_safe mysqld from pid file /var/run/mysqld/mysql.pid ended

The announcement of the MySQL Yum repositories was a long overdue request on my wish list. While it was possible to find MySQL at http://public-yum.oracle.com/ it was not the GA version MySQL 5.6. (As I write this post, I check and find that indeed it now appears this may be possible http://public-yum.oracle.com/repo/OracleLinux/OL6/MySQL56/).

I have previously installed MySQL 5.6.13 via rpms downloaded from MySQL Downloads, so I expected the upgrade to be straightforward. Following Chapter 3. Upgrading MySQL with the MySQL Yum Repository I had no success.

$ sudo yum update mysql-server
Loaded plugins: fastestmirror, presto
Loading mirror speeds from cached hostfile
 * base: mirror.lug.udel.edu
 * extras: mirror.cisp.com
 * updates: centos.mirror.constant.com
Setting up Update Process
Package(s) mysql-server available, but not installed.
No Packages marked for Update

Looking at what information is available for the mysql-server package (This is the package name specified at Chapter 1. Installing MySQL on Linux Using the MySQL Yum Repository I find.

$ sudo yum info mysql-server
Loaded plugins: fastestmirror, presto
Loading mirror speeds from cached hostfile
* base: mirror.lug.udel.edu
* extras: mirror.cisp.com
* updates: centos.mirror.constant.com
Installed Packages
Name : MySQL-server
Arch : x86_64
Version : 5.6.13
Release : 1.el6
Size : 235 M
Repo : installed
Summary : MySQL: a very fast and reliable SQL database server
…
Available Packages
Name : mysql-server
Arch : x86_64
Version : 5.1.69
Release : 1.el6_4
Size : 8.7 M
Repo : updates

This DOES NOT actually show what I would expect. I had to in fact search for mysql-community-server (NOTE: I discovered this as a note after the previously mentioned package name This installs the package for MySQL server (mysql-community-server) and also packages).

$ sudo yum info mysql-community-server
Loaded plugins: fastestmirror, presto
Loading mirror speeds from cached hostfile
* base: mirror.lug.udel.edu
* extras: mirror.cisp.com
* updates: centos.mirror.constant.com
Available Packages
Name : mysql-community-server
Arch : x86_64
Version : 5.6.14
Release : 3.el6
Size : 51 M
Repo : mysql-community

I suspect I cannot update this (as it’s not actually installed), which is confirmed with.

$ sudo yum update mysql-community-server
Loaded plugins: fastestmirror, presto
Loading mirror speeds from cached hostfile
 * base: mirror.lug.udel.edu
 * extras: mirror.cisp.com
 * updates: centos.mirror.constant.com
Setting up Update Process
Package(s) mysql-community-server available, but not installed.
No Packages marked for Update

So, I am left wit the option of installing this (again I’m not confident), and again confirmed.

$ sudo yum install mysql-community-server
Loaded plugins: fastestmirror, presto
Loading mirror speeds from cached hostfile
 * base: mirror.lug.udel.edu
 * extras: mirror.cisp.com
 * updates: centos.mirror.constant.com
Setting up Install Process
Resolving Dependencies
--> Running transaction check
---> Package mysql-community-server.x86_64 0:5.6.14-3.el6 will be installed
--> Processing Dependency: mysql-community-common(x86-64) = 5.6.14-3.el6 for package: mysql-community-server-5.6.14-3.el6.x86_64
--> Processing Dependency: mysql-community-client(x86-64) = 5.6.14-3.el6 for package: mysql-community-server-5.6.14-3.el6.x86_64
--> Running transaction check
---> Package mysql-community-client.x86_64 0:5.6.14-3.el6 will be installed
--> Processing Dependency: mysql-community-libs(x86-64) = 5.6.14-3.el6 for package: mysql-community-client-5.6.14-3.el6.x86_64
---> Package mysql-community-common.x86_64 0:5.6.14-3.el6 will be installed
--> Running transaction check
---> Package mysql-community-libs.x86_64 0:5.6.14-3.el6 will be installed
--> Finished Dependency Resolution

Dependencies Resolved

=======================================================================================================================================================================
 Package                                         Arch                            Version                                Repository                                Size
=======================================================================================================================================================================
Installing:
 mysql-community-server                          x86_64                          5.6.14-3.el6                           mysql-community                           51 M
Installing for dependencies:
 mysql-community-client                          x86_64                          5.6.14-3.el6                           mysql-community                           18 M
 mysql-community-common                          x86_64                          5.6.14-3.el6                           mysql-community                          296 k
 mysql-community-libs                            x86_64                          5.6.14-3.el6                           mysql-community                          1.8 M

Transaction Summary
=======================================================================================================================================================================
Install       4 Package(s)

Total download size: 71 M
Installed size: 321 M
Is this ok [y/N]: y
Downloading Packages:
Setting up and reading Presto delta metadata
Processing delta metadata
Package(s) data still to download: 71 M
(1/4): mysql-community-client-5.6.14-3.el6.x86_64.rpm                                                                                           |  18 MB     00:00
(2/4): mysql-community-common-5.6.14-3.el6.x86_64.rpm                                                                                           | 296 kB     00:00
(3/4): mysql-community-libs-5.6.14-3.el6.x86_64.rpm                                                                                             | 1.8 MB     00:00
(4/4): mysql-community-server-5.6.14-3.el6.x86_64.rpm                                                                                           |  51 MB     00:02
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------
Total                                                                                                                                   21 MB/s |  71 MB     00:03
warning: rpmts_HdrFromFdno: V3 DSA/SHA1 Signature, key ID 5072e1f5: NOKEY
Retrieving key from file:///etc/pki/rpm-gpg/RPM-GPG-KEY-mysql
Importing GPG key 0x5072E1F5:
 Userid : MySQL Release Engineering 
 Package: mysql-community-release-el6-3.noarch (@/mysql-community-release-el6-3.noarch)
 From   : /etc/pki/rpm-gpg/RPM-GPG-KEY-mysql
Is this ok [y/N]: y
Running rpm_check_debug
Running Transaction Test


Transaction Check Error:
  file /usr/bin/mysql_config from install of mysql-community-client-5.6.14-3.el6.x86_64 conflicts with file from package MySQL-devel-5.6.13-1.el6.x86_64
  file /usr/bin/mysql from install of mysql-community-client-5.6.14-3.el6.x86_64 conflicts with file from package MySQL-client-5.6.13-1.el6.x86_64
...
  file /usr/share/mysql/errmsg-utf8.txt from install of mysql-community-common-5.6.14-3.el6.x86_64 conflicts with file from package MySQL-server-5.6.13-1.el6.x86_64

Error Summary
-------------

At this time I believe it’s not possible to update from official MySQL rpms to the official yum repository, which is rather disappointing. I would have assumed this was a test case. Hopefully, somebody with better package management skills can shed some light!

MySQL Yum Repository Installation

The following steps were used to Install the MySQL repository.

$ cd /tmp
$ wget http://repo.mysql.com/mysql-community-release-el6-3.noarch.rpm
$ sudo yum localinstall mysql-community-release-el6-3.noarch.rpm
$ sudo yum repolist enabled | grep “mysql-community”

A trap for those new to the MySQL Performance Schema is the expectation that thread_id in tables such as events_statements_current matches the id you find in the MySQL processlist. This is NOT TRUE.

If we look at the INFORMATION_SCHEMA.PROCESSLIST table we will find information like:

mysql> select id,db,command,state from information_schema.processlist order by id;
-----------+--------------------+---------+------------------------------------------------------------------+
| id        | db                 | command | state                                                            |
+-----------+--------------------+---------+------------------------------------------------------------------+
|         1 | NULL               | Connect | Slave has read all relay log; waiting for the slave I/O thread t |
|         2 | NULL               | Connect | Waiting for master to send event                                 |
|         5 | NULL               | Sleep   |                                                                  |
|  34404870 | NULL               | Sleep   |                                                                  |
| 106759077 | performance_schema | Sleep   |                                                                  |
| 106904549 | performance_schema | Query   | executing                                                        |
| 107004213 | abc                | Sleep   |                                                                  |
| 107004600 | abc                | Sleep   |                                                                  |
| 107004877 | abc                | Sleep   |                                                                  |
| 107004937 | abc                | Sleep   |                                                                  |
| 107004989 | abc                | Sleep   |                                                                  |
| 107005164 | abc                | Sleep   |                                                                  |
| 107005305 | abc                | Sleep   |                                                                  |
| 107005310 | abc                | Sleep   |                                                                  |
| 107005314 | abc                | Sleep   |                                                                  |
| 107005316 | abc                | Sleep   |                                                                  |
| 107005317 | abc                | Sleep   |                                                                  |
| 107005321 | abc                | Sleep   |                                                                  |
+-----------+--------------------+---------+------------------------------------------------------------------+

However, if I wanted to look at the two slave threads in performance_schema.events_statements_current I will find no matching data.

mysql> select * from performance_schema.events_statements_current where thread_id=1;
Empty set (0.00 sec)
mysql> select * from performance_schema.events_statements_current where thread_id=2;
Empty set (0.00 sec)

In the performance schema, you need to use the threads table in order to determine a match between the processlist and the threads. If we look at the table, you will find information about all the BACKGROUND threads in MySQL.

mysql> select thread_id,name,type,processlist_id from threads;
+-----------+----------------------------------------+------------+----------------+
| thread_id | name                                   | type       | processlist_id |
+-----------+----------------------------------------+------------+----------------+
|         1 | thread/sql/main                        | BACKGROUND |           NULL |
|         2 | thread/innodb/io_handler_thread        | BACKGROUND |           NULL |
|         3 | thread/innodb/io_handler_thread        | BACKGROUND |           NULL |
|         4 | thread/innodb/io_handler_thread        | BACKGROUND |           NULL |
|         5 | thread/innodb/io_handler_thread        | BACKGROUND |           NULL |
|         6 | thread/innodb/io_handler_thread        | BACKGROUND |           NULL |
|         7 | thread/innodb/io_handler_thread        | BACKGROUND |           NULL |
|         8 | thread/innodb/io_handler_thread        | BACKGROUND |           NULL |
|         9 | thread/innodb/io_handler_thread        | BACKGROUND |           NULL |
|        10 | thread/innodb/io_handler_thread        | BACKGROUND |           NULL |
|        11 | thread/innodb/io_handler_thread        | BACKGROUND |           NULL |
|        12 | thread/innodb/io_handler_thread        | BACKGROUND |           NULL |
|        13 | thread/innodb/io_handler_thread        | BACKGROUND |           NULL |
|        14 | thread/innodb/io_handler_thread        | BACKGROUND |           NULL |
|        15 | thread/innodb/io_handler_thread        | BACKGROUND |           NULL |
|        17 | thread/innodb/srv_lock_timeout_thread  | BACKGROUND |           NULL |
|        18 | thread/innodb/srv_error_monitor_thread | BACKGROUND |           NULL |
|        19 | thread/innodb/srv_monitor_thread       | BACKGROUND |           NULL |
|        20 | thread/innodb/srv_master_thread        | BACKGROUND |           NULL |
|        21 | thread/innodb/srv_purge_thread         | BACKGROUND |           NULL |
|        22 | thread/innodb/page_cleaner_thread      | BACKGROUND |           NULL |
|        23 | thread/sql/signal_handler              | BACKGROUND |           NULL |
|        24 | thread/sql/slave_io                    | BACKGROUND |           NULL |
|        25 | thread/sql/slave_sql                   | BACKGROUND |           NULL |
|        28 | thread/sql/one_connection              | FOREGROUND |              5 |
| 107013952 | thread/sql/one_connection              | FOREGROUND |      107013929 |
| 107013989 | thread/sql/one_connection              | FOREGROUND |      107013966 |
| 106759100 | thread/sql/one_connection              | FOREGROUND |      106759077 |
| 107014180 | thread/sql/one_connection              | FOREGROUND |      107014157 |
| 107014291 | thread/sql/one_connection              | FOREGROUND |      107014268 |
| 106904572 | thread/sql/one_connection              | FOREGROUND |      106904549 |
| 107014443 | thread/sql/one_connection              | FOREGROUND |      107014420 |
| 107014490 | thread/sql/one_connection              | FOREGROUND |      107014467 |
| 107014491 | thread/sql/one_connection              | FOREGROUND |      107014468 |
| 107014493 | thread/sql/one_connection              | FOREGROUND |      107014470 |
| 107014497 | thread/sql/one_connection              | FOREGROUND |      107014474 |
| 107014498 | thread/sql/one_connection              | FOREGROUND |      107014475 |
|  34404893 | thread/sql/one_connection              | FOREGROUND |       34404870 |
| 107013233 | thread/sql/one_connection              | FOREGROUND |      107013210 |
+-----------+----------------------------------------+------------+----------------+
39 rows in set (0.00 sec)

While it’s great the performance schema can track the statements executed in the Slave SQL thread (I’ll discuss that later), it’s disappointing that the processlist_id, the one thing that can join our two sources of data other, has not value for the slave threads.

mysql> select * from threads where thread_id=25G
*************************** 1. row ***************************
          THREAD_ID: 25
               NAME: thread/sql/slave_sql
               TYPE: BACKGROUND
     PROCESSLIST_ID: NULL
   PROCESSLIST_USER: NULL
   PROCESSLIST_HOST: NULL
     PROCESSLIST_DB: NULL
PROCESSLIST_COMMAND: NULL
   PROCESSLIST_TIME: 0
  PROCESSLIST_STATE: Slave has read all relay log; waiting for the slave I/O thread t
   PROCESSLIST_INFO: NULL
   PARENT_THREAD_ID: 1
               ROLE: NULL
       INSTRUMENTED: YES
1 row in set (0.00 sec)

For normal queries we can get a relationship between the processlist and the performance schema with:

select p.id,p.db,p.command,p.state,s.*
from information_schema.processlist p
inner join performance_schema.threads t on p.id = t.processlist_id
inner join performance_schema. events_statements_current s using (thread_id)
where p.command='Query'G
...
*************************** 2. row ***************************
                     id: 106904549
                     db: performance_schema
                command: Query
                  state: executing
              THREAD_ID: 106904572
               EVENT_ID: 78
           END_EVENT_ID: NULL
             EVENT_NAME: statement/sql/select
                 SOURCE: mysqld.cc:931
            TIMER_START: 268504759200898000
              TIMER_END: NULL
             TIMER_WAIT: NULL
              LOCK_TIME: 580000000
               SQL_TEXT: select p.id,p.db,p.command,p.state,s.* from information_schema.processlist p inner join performance_schema.threads t on p.id = t.processlist_id inner join performance_schema. events_statements_current s using (thread_id) where p.command='Query'
                 DIGEST: NULL
            DIGEST_TEXT: NULL
         CURRENT_SCHEMA: performance_schema
            OBJECT_TYPE: NULL
          OBJECT_SCHEMA: NULL
            OBJECT_NAME: NULL
  OBJECT_INSTANCE_BEGIN: NULL
            MYSQL_ERRNO: 0
      RETURNED_SQLSTATE: NULL
           MESSAGE_TEXT: NULL
                 ERRORS: 0
               WARNINGS: 0
          ROWS_AFFECTED: 0
              ROWS_SENT: 1
          ROWS_EXAMINED: 0
CREATED_TMP_DISK_TABLES: 1
     CREATED_TMP_TABLES: 1
       SELECT_FULL_JOIN: 2
 SELECT_FULL_RANGE_JOIN: 0
           SELECT_RANGE: 0
     SELECT_RANGE_CHECK: 0
            SELECT_SCAN: 1
      SORT_MERGE_PASSES: 0
             SORT_RANGE: 0
              SORT_ROWS: 0
              SORT_SCAN: 0
          NO_INDEX_USED: 1
     NO_GOOD_INDEX_USED: 0
       NESTING_EVENT_ID: NULL

Using MySQL 5.6.13 under CentOS 6.4, I had a replication failure on one master/slave topology because the master binary log had the following entry that was intentionally written by the MySQL server.

$ mysqlbinlog --start-position=244670849 mysql-bin.000029
...
# at 244670849
#131028 19:31:38 server id 39  end_log_pos 244670906 CRC32 0xc5d084ec
# Incident: LOST_EVENTS
RELOAD DATABASE; # Shall generate syntax error
# at 244670906
...

The question is why? I do not know the answer. Searching online indicates this can occur in a MySQL Cluster environment, and can occur around the use of GRANT statements. Neither of these situations are applicable here. This site runs 4 different master/slave topologies all running the same version, and this has been the only occurrence.

The message, if taken literally could indicate that the master server failed to write all events to the master binary log, but instead of reporting any information (say in the MySQL error log), it basically tells you the binary log (aka the replication stream) is now incomplete and you need to rebuild your entire replication topology. If this is true, then this is a poor explanation, and there is no MySQL documentation I have found to shed light here.

The situation of course does not manifest to the end user on the master (or say monitoring the MySQL error log), but on the slave with a message similar to:

mysql> SHOW SLAVE STATUSG
...
        Relay_Master_Log_File: mysql-bin.000029
          Exec_Master_Log_Pos: 244670849
...
             Slave_IO_Running: Yes
            Slave_SQL_Running: No
                   Last_Errno: 1590
                   Last_Error: The incident LOST_EVENTS occured on the master. Message: error writing to the binary log
...

What appears to happen on the master, is the LOST_EVENTS binary log event is written, the binary logs are flushed, as indicated by the file sizes.

-rw-rw---- 1 mysql mysql 1073742236 Oct 27 23:33 mysql-bin.000027
-rw-rw---- 1 mysql mysql 1073741890 Oct 28 11:28 mysql-bin.000028
-rw-rw---- 1 mysql mysql  244670953 Oct 28 19:31 mysql-bin.000029
-rw-rw---- 1 mysql mysql 1073742184 Oct 29 08:55 mysql-bin.000030

Further analysis of the statements before the event in the master log show nothing of incident. Analysis of the binary logs at the error and subsequently how second timestamps that are identical, so there is no *obvious* loss of operations, but when there are 100s of transactions per second, using second granularity is ineffective.

When confirming there were no events after this position on the slave, and the binary logs had been flushed the solution taken was to reset the slave to the next valid event.

mysql> STOP SLAVE;
mysql> CHANGE MASTER TO MASTER_LOG_FILE='mysql-bin.000030', MASTER_LOG_POS=120;
mysql> START SLAVE:

Help, the database is on fire. Well, it probably is but the solution may also be easy. Here are a few steps for the part-time MySQL DBA/sysadmin/developer. Total time to address this solution was 2 minutes, the inability to not go back to sleep, not priceless.

First, access to the DB server is possible, and also the mysql command line client. If you are getting “Too Many Connections” read Why GRANT ALL is bad.

Given the message “the database is on fire”, the likely cause is rogue SQL.

mysql> show global variables like 'max_connections';
+-----------------+-------+
| Variable_name   | Value |
+-----------------+-------+
| max_connections | 5000  |
+-----------------+-------+
1 row in set (0.02 sec)

mysql> show global status like 'threads%';
+-------------------+-------+
| Variable_name     | Value |
+-------------------+-------+
| Threads_cached    | 1     |
| Threads_connected | 5001  |
| Threads_created   | 5002  |
| Threads_running   | 5001  |
+-------------------+-------+
4 rows in set (0.01 sec)

Yeah, as expected. A SHOW PROCESSLIST in this situation shows all queries stuck in the state of “query end”, which indicates the obvious problem to me (a disk space problem).

For the record I do not recommend setting max_connections to 5,000. MySQL (and Linux) does not function with 5,000 concurrent connections (especially when they all want to create a disk based temporary table, but that’s another story). What is missing is a maximum threads running configuration option, and applicable coding practices and proactive server connection management to prevent such a situation.

Confirming my suspicions.

$ df -h
Filesystem            Size  Used Avail Use% Mounted on
/dev/xvde             7.9G  2.5G  5.0G  34% /
tmpfs                 7.3G     0  7.3G   0% /dev/shm
/dev/xvdf1            197G   42G  146G  23% /mysql
/dev/xvdh1             99G   94G  8.0K 100% /mysql/binlog

The solution here is simple, you need to remove old binary logs. It is NOT the recommendation you delete the files manually but use PURGE MASTER LOGS. However this produced an error.

mysql> purge master logs to 'mysql-bin.000029';
ERROR 3 (HY000): Error writing file '/mysql/binlog/mysql-bin.index_crash_safe' (Errcode: 28 - No space left on device)

That’s a new message, possibly a new MySQL 5.6 error situation. The only choice now is to remove a physical file first. A suggestion to MySQL engineers. Let’s create this file in normal operations with sufficient blank bytes, enabling MySQL to be able to create the file even when the disk is full, and then avoid manual file manipulation.

$ rm mysql-bin.000002

Then:

mysql> purge master logs to 'mysql-bin.000029';
Query OK, 0 rows affected, 1 warning (1.37 sec)
mysql> show warnings;
+---------+------+---------------------------------------------------------------+
| Level   | Code | Message                                                       |
+---------+------+---------------------------------------------------------------+
| Warning | 1612 | Being purged log /mysql/binlog/mysql-bin.000002 was not found |
+---------+------+---------------------------------------------------------------+
1 row in set (0.01 sec)

As always, a recommendation when problems occur is to check the error log (aka Monitoring the MySQL Error Log). This issue is also immediately apparent.

2013-08-23 06:28:36 30609 [Warning] Disk is full writing '/mysql/binlog/mysql-bin.000097' (Errcode: 28 - No space left on device). Waiting for someone to free space...
2013-08-23 06:28:36 30609 [Warning] Retry in 60 secs. Message reprinted in 600 secs

I would also like to point out that being proactive and having monitoring and instrumentation in ALL startups is critical if you want to be successful. Point 1 in my recommendations of Successful Scalability Principles.

Was it really an emergency?

The following simple INFORMATION_SCHEMA statement will identify and also verify tables that have no rows. These may be candidate tables to remove from your data model.

mysql --defaults-file=.my.cnf -N -e "select CONCAT('SELECT "',table_schema,'.',table_name,'" AS tbl, COUNT(*) AS cnt FROM ',table_schema,'.',table_name,';') as cmd from information_schema.tables where table_schema not in ('mysql','performance_schema','information_schema') and table_rows=0;" | mysql --defaults-file=.my.cnf -N

I setup 6 shiny new MySQL 5.6.13 MySQL servers, ready for testing and production deployment tomorrow.

I found that the New Relic MySQL Monitoring was throwing the following error.

[2013-08-08 03:53:33 +0000] com.newrelic.plugins.mysql.MySQL | SEVERE | An SQL error occured running 'SHOW ENGINE INNODB STATUS' Access denied; you need (at least one of) the PROCESS privilege(s) for this operation

Simple fix, the user I am gathering metrics requires the PROCESS privilege. Again simple enough.

mysql> grant PROCESS on xxx.* to xxx@'10.%';
ERROR 1221 (HY000): Incorrect usage of DB GRANT and GLOBAL PRIVILEGES
mysql> grant PROCESS on *.* to xxx@'10.%';
Query OK, 0 rows affected (0.00 sec)

As you can see I got an error for a global privilege, again trivial, easy fix to correct syntax. However, it breaks replication with a very non descriptive message.

mysql> SHOW SLAVE STATUSG
...
Last_Errno: 1590
Last_Error: The incident LOST_EVENTS occured on the master. Message: error writing to the binary log
...

Bug #68892 reported this in April, verified by Oracle support, but is listed as ‘non-critical’. I agree with the bug author, given MySQL 5.6 touts many MySQL replication improvements, a simple failed statement should not break replication.

As part of uncovering a new security improvement in MySQL 5.6 with the default installation being secured with a unique root MySQL password, the MySQL provided rpm’s installed the MySQL configuration file in /usr.

I feel this maybe a bug, however this is just as an explanation for others to comment on.
The following steps reproduces this.

1. Launch a CentOS 6.4 AWS EC2 Instance

LOG=/tmp/create-instance.tmp.$$
INSTANCE_TYPE=m1.medium
ec2-run-instances ami-eb6b0182 --instance-type ${INSTANCE_TYPE} --region us-east-1 --availability-zone us-east-1b --key db --group db | tee ${LOG}
INSTANCE=`grep ^INSTANCE ${LOG} | awk '{print $2}'`
ec2-describe-instances ${INSTANCE} | tee ${LOG}
while [ `grep ^INSTANCE ${LOG} | awk '{print $6}'` != 'running' ] ;  do cat ${LOG}; sleep 5; ec2-describe-instances ${INSTANCE} | tee ${LOG}; done
SERVER=`grep ^INSTANCE ${LOG} | awk '{print $4}'`
echo "#instance=${INSTANCE},server=${SERVER}"

#instance=i-xxx,server=ec2-xxx.compute-1.amazonaws.com

2. Connect to server

ssh -i ~/.ssh/db.pem [email protected]

3. Install software

yum update -y

# Remove the Postfix MySQL dependency
rpm -qa | grep -i mysql
rpm -e --nodeps mysql-libs-5.1.69-1.el6_4.x86_64

# Just to prove no config here
ls -l /etc/my.cnf
ls: cannot access /etc/my.cnf: No such file or directory
ls -l /usr/my.cnf
ls: cannot access /usr/my.cnf: No such file or directory

# Install MySQL prerequisites
yum install -y libaio perl

cd /tmp
yum install -y wget
wget http://cdn.mysql.com/Downloads/MySQL-5.6/MySQL-5.6.13-1.el6.x86_64.rpm-bundle.tar
tar xvf MySQL-5.6.13-1.el6.x86_64.rpm-bundle.tar
rpm -ivh MySQL*.rpm

4. The results of the installation of the default MySQL 5.6 rpms.

A RANDOM PASSWORD HAS BEEN SET FOR THE MySQL root USER !
You will find that password in '/root/.mysql_secret'.

You must change that password on your first connect,
no other statement but 'SET PASSWORD' will be accepted.
See the manual for the semantics of the 'password expired' flag.

Also, the account for the anonymous user has been removed.

In addition, you can run:

  /usr/bin/mysql_secure_installation

which will also give you the option of removing the test database.
This is strongly recommended for production servers.

See the manual for more instructions.

Please report any problems with the /usr/bin/mysqlbug script!

The latest information about MySQL is available on the web at

http://www.mysql.com

Support MySQL by buying support/licenses at http://shop.mysql.com

New default config file was created as /usr/my.cnf and
will be used by default by the server when you start it.
You may edit this file to change server settings

As you can see via the rpm installation instructions, a new configuration file was created in “/usr/my.cnf”

$ cat /usr/my.cnf
# For advice on how to change settings please see
# http://dev.mysql.com/doc/refman/5.6/en/server-configuration-defaults.html

[mysqld]

# Remove leading # and set to the amount of RAM for the most important data
# cache in MySQL. Start at 70% of total RAM for dedicated server, else 10%.
# innodb_buffer_pool_size = 128M

# Remove leading # to turn on a very important data integrity option: logging
# changes to the binary log between backups.
# log_bin

# These are commonly set, remove the # and set as required.
# basedir = .....
# datadir = .....
# port = .....
# server_id = .....
# socket = .....

# Remove leading # to set options mainly useful for reporting servers.
# The server defaults are faster for transactions and fast SELECTs.
# Adjust sizes as needed, experiment to find the optimal values.
# join_buffer_size = 128M
# sort_buffer_size = 2M
# read_rnd_buffer_size = 2M

sql_mode=NO_ENGINE_SUBSTITUTION,STRICT_TRANS_TABLES

By default the included Lua within MySQL proxy (0.8.3) does not include socket, necessary for getting microsecond granularity. To setup you have to install Lua and socket on the OS first:

For CentO5

$ sudo yum install lua lua-socket

For Ubuntu

$ sudo apt-get install lua5.1 liblua5.1-socket2

The following enables use within MySQL Proxy.

cp /usr/share/lua/5.1/socket.lua /path/to/mysqlproxy/lib/mysql-proxy/lua
cp -r /usr/lib64/lua/5.1/socket /path/to/mysqlproxy/lib/mysql-proxy/lua
cp -r /usr/lib64/lua/5.1/mime /path/to/mysqlproxy/lib/mysql-proxy/lua

My lua script can now use syntax similar to:

require 'socket'

function read_query( packet )
...
  now=socket.gettime()
  print( string.format("# %s.%3dn%s;n",os.date("%X",now),select(2,math.modf(now))*1000 , query))