Reviewing your MySQL installation on Oracle Enterprise Linux

After successfully Installing MySQL, let us take a look at an operational MySQL instance on your Oracle Enterprise Linux server.

User Management

By default there will be a new mysql user and group created. This user is used to run the mysqld process is generally not used for any other purpose.

$ grep mysql /etc/{passwd,shadow,group}
/etc/passwd:mysql:x:27:27:MySQL Server:/var/lib/mysql:/bin/bash
/etc/shadow:mysql:!!:14796::::::
/etc/group:mysql:x:27:

Binaries

MySQL binaries are found in /usr/bin.

$ ls -l /usr/bin/mysql*
-rwxr-xr-x 1 root root  314568 Feb 16 17:45 /usr/bin/mysql
-rwxr-xr-x 1 root root  110776 Feb 16 14:39 /usr/bin/mysqlaccess
-rwxr-xr-x 1 root root   35144 Feb 16 17:45 /usr/bin/mysqladmin
-rwxr-xr-x 1 root root  112944 Feb 16 17:45 /usr/bin/mysqlbinlog
-rwxr-xr-x 1 root root    7632 Feb 16 17:45 /usr/bin/mysqlbug
-rwxr-xr-x 1 root root   30576 Feb 16 17:45 /usr/bin/mysqlcheck
-rwxr-xr-x 1 root root    7632 Feb 16 17:45 /usr/bin/mysql_config
-rwxr-xr-x 1 root root    3670 Feb 16 17:44 /usr/bin/mysql_convert_table_format
-rwxr-xr-x 1 root root   22522 Feb 16 17:44 /usr/bin/mysqld_multi
-rwxr-xr-x 1 root root   13073 Feb 16 17:44 /usr/bin/mysqld_safe
-rwxr-xr-x 1 root root   75184 Feb 16 17:45 /usr/bin/mysqldump
-rwxr-xr-x 1 root root    6356 Feb 16 17:44 /usr/bin/mysqldumpslow
-rwxr-xr-x 1 root root   11648 Feb 16 17:44 /usr/bin/mysql_explain_log
-rwxr-xr-x 1 root root    3245 Feb 16 14:39 /usr/bin/mysql_find_rows
-rwxr-xr-x 1 root root     483 Feb 16 17:44 /usr/bin/mysql_fix_extensions
-rwxr-xr-x 1 root root    5834 Feb 16 17:44 /usr/bin/mysql_fix_privilege_tables
-rwxr-xr-x 1 root root   31431 Feb 16 17:44 /usr/bin/mysqlhotcopy
-rwxr-xr-x 1 root root   26160 Feb 16 17:45 /usr/bin/mysqlimport
-rwxr-xr-x 1 root root   13659 Feb 16 17:44 /usr/bin/mysql_install_db
-rwxr-xr-x 1 root root    6586 Feb 16 17:44 /usr/bin/mysql_secure_installation
-rwxr-xr-x 1 root root   16687 Feb 16 17:44 /usr/bin/mysql_setpermission
-rwxr-xr-x 1 root root   28224 Feb 16 17:45 /usr/bin/mysqlshow
-rwxr-xr-x 1 root root   14473 Feb 16 14:39 /usr/bin/mysql_tableinfo
-rwxr-xr-x 1 root root  158192 Feb 16 17:45 /usr/bin/mysqltest
-rwxr-xr-x 1 root root   42360 Feb 16 17:45 /usr/bin/mysqltestmanager
-rwxr-xr-x 1 root root   15464 Feb 16 17:45 /usr/bin/mysqltestmanagerc
-rwxr-xr-x 1 root root   13448 Feb 16 17:45 /usr/bin/mysqltestmanager-pwgen
-rwxr-xr-x 1 root root 1312064 Feb 16 17:45 /usr/bin/mysql_tzinfo_to_sql
-rwxr-xr-x 1 root root   54160 Feb 16 17:45 /usr/bin/mysql_upgrade
-rwxr-xr-x 1 root root    5753 Feb 16 17:44 /usr/bin/mysql_upgrade_shell
-rwxr-xr-x 1 root root  112136 Feb 16 17:45 /usr/bin/mysql_waitpid
-rwxr-xr-x 1 root root    3818 Feb 16 17:44 /usr/bin/mysql_zap

The mysqld binary is found in /usr/libexec

Error Log

The MySQL error log is found in /var/log/mysqld.log

The content after an initial start of MySQL will look similar to:

cat /var/log/mysqld.log
100705 22:09:03  mysqld started
InnoDB: The first specified data file ./ibdata1 did not exist:
InnoDB: a new database to be created!
100705 22:09:03  InnoDB: Setting file ./ibdata1 size to 10 MB
InnoDB: Database physically writes the file full: wait...
100705 22:09:03  InnoDB: Log file ./ib_logfile0 did not exist: new to be created
InnoDB: Setting log file ./ib_logfile0 size to 5 MB
InnoDB: Database physically writes the file full: wait...
100705 22:09:03  InnoDB: Log file ./ib_logfile1 did not exist: new to be created
InnoDB: Setting log file ./ib_logfile1 size to 5 MB
InnoDB: Database physically writes the file full: wait...
InnoDB: Doublewrite buffer not found: creating new
InnoDB: Doublewrite buffer created
InnoDB: Creating foreign key constraint system tables
InnoDB: Foreign key constraint system tables created
100705 22:09:03  InnoDB: Started; log sequence number 0 0
100705 22:09:03 [Note] /usr/libexec/mysqld: ready for connections.
Version: '5.0.77'  socket: '/var/lib/mysql/mysql.sock'  port: 3306  Source distribution

On the first invocation of MySQL, the InnoDB storage engine will create a default tablespace and redo logs. This is the majority of messages in the above log.

Processes

MySQL is a multi-threaded single process called mysqld. A second wrapper process mysqld_safe is generally found. This process logs stderr and also will restart the mysqld process if not found.

ps -ef | grep mysql
root     14733     1  0 Jul05 pts/1    00:00:00 /bin/sh /usr/bin/mysqld_safe --datadir=/var/lib/mysql --socket=/var/lib/mysql/mysql.sock --log-error=/var/log/mysqld.log --pid-file=/var/run/mysqld/mysqld.pid --user=mysql
mysql    14783 14733  0 Jul05 pts/1    00:00:10 /usr/libexec/mysqld --basedir=/usr --datadir=/var/lib/mysql --user=mysql --pid-file=/var/run/mysqld/mysqld.pid --skip-external-locking --socket=/var/lib/mysql/mysql.sock

Memory Usage

MySQL can have a very low memory footprint. By default the mysqld process has a 175M virtual size.

$ ps -eopid,fname,rss,vsz,user,command | grep -e "RSS" -e "mysql"
  PID COMMAND    RSS    VSZ USER     COMMAND
14275 grep       720  61136 root     grep -e RSS -e mysql
14733 mysqld_s  1192  63820 root     /bin/sh /usr/bin/mysqld_safe --datadir=/var/lib/mysql --socket=/var/lib/mysql/mysql.sock --log-error=/var/log/mysqld.log --pid-file=/var/run/mysqld/mysqld.pid --user=mysql
14783 mysqld   27004 179496 mysql    /usr/libexec/mysqld --basedir=/usr --datadir=/var/lib/mysql --user=mysql --pid-file=/var/run/mysqld/mysqld.pid --skip-external-locking --socket=/var/lib/mysql/mysql.sock

Disk Usage

The MySQL data files will be stored on a default installation in /var/lib/mysql

$ du -sh /var/lib/mysql
22M     /var/lib/mysql

$ ls -ld /var/lib/mysql
drwxr-xr-x 4 mysql mysql 4096 Jul 13 11:50 /var/lib/mysql

$ ls -l /var/lib/mysql
total 20552
-rw-rw---- 1 mysql mysql 10485760 Jul  5 22:09 ibdata1
-rw-rw---- 1 mysql mysql  5242880 Jul  5 22:09 ib_logfile0
-rw-rw---- 1 mysql mysql  5242880 Jul  5 22:09 ib_logfile1
drwx------ 2 mysql mysql     4096 Jul  5 22:09 mysql
srwxrwxrwx 1 mysql mysql        0 Jul  5 22:09 mysql.sock

The MySQL data directory includes the InnoDB tablespace datafile (ibdata1), redo logs (ib_logfile?), and the mysql directory corresponding to the mysql schema containing instance meta data.

This directory also contains the socket file, which is actually a poor location as this opens the security of this directory for world access. This will be discussed later in securing your installation.

Running MySQL

The best means of controlling the starting and stopping of mysql is to use the provided service init script mysqld

$ ls -l /etc/init.d/mysqld
-rwxr-xr-x 1 root root 4286 Feb 16 17:45 /etc/init.d/mysqld

Configuration

For OEL the MySQL configuration can be found in /etc.
NOTE: MySQL can use multiple configuration files.

$ ls -l /etc/my.cnf
-rw-r--r-- 1 root root 441 Feb 16 14:39 /etc/my.cnf

MySQL includes a minimalistic configuration file by default. The configuration file format is variable=value pairs for a given number of different sections, in this file [mysqld] and [mysqld_safe].

$ cat /etc/my.cnf

[mysqld]
datadir=/var/lib/mysql
socket=/var/lib/mysql/mysql.sock
user=mysql
# Default to using old password format for compatibility with mysql 3.x
# clients (those using the mysqlclient10 compatibility package).
old_passwords=1

# Disabling symbolic-links is recommended to prevent assorted security risks;
# to do so, uncomment this line:
# symbolic-links=0

[mysqld_safe]
log-error=/var/log/mysqld.log
pid-file=/var/run/mysqld/mysqld.pid

Audit

A full audit of all MySQL related files.

find / -name "*mysql*"
/etc/rc.d/rc3.d/S64mysqld
/etc/rc.d/rc5.d/S64mysqld
/etc/rc.d/rc6.d/K36mysqld
/etc/rc.d/init.d/mysqld
/etc/rc.d/rc0.d/K36mysqld
/etc/rc.d/rc4.d/S64mysqld
/etc/rc.d/rc1.d/K36mysqld
/etc/rc.d/rc2.d/S64mysqld
/etc/php.d/pdo_mysql.ini
/etc/php.d/mysql.ini
/etc/php.d/mysqli.ini
/etc/ld.so.conf.d/mysql-x86_64.conf
/etc/ld.so.conf.d/mysql-i386.conf
/usr/lib64/mysql
/usr/lib64/mysql/mysqlbug
/usr/lib64/mysql/libmysqlclient_r.so.15.0.0
/usr/lib64/mysql/libmysqlclient.so.15
/usr/lib64/mysql/libmysqlclient_r.so.15
/usr/lib64/mysql/mysql_config
/usr/lib64/mysql/libmysqlclient.so.15.0.0
/usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi/Bundle/DBD/mysql.pm
/usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi/auto/DBD/mysql
/usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi/auto/DBD/mysql/mysql.so
/usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi/DBD/mysql
/usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi/DBD/mysql.pm
/usr/lib64/php/modules/mysql.so
/usr/lib64/php/modules/pdo_mysql.so
/usr/lib64/php/modules/mysqli.so
/usr/libexec/mysqld
/usr/libexec/mysqlmanager
/usr/share/mysql
/usr/share/mysql/mysql_system_tables.sql
/usr/share/mysql/mysql_system_tables_data.sql
/usr/share/mysql/mysql_fix_privilege_tables.sql
/usr/share/mysql/mysql_test_data_timezone.sql
/usr/share/vim/vim70/syntax/mysql.vim
/usr/share/man/man8/mysqld.8.gz
/usr/share/man/man8/mysqlmanager.8.gz
/usr/share/man/man1/mysql.1.gz
/usr/share/man/man1/mysql.server.1.gz
/usr/share/man/man1/mysql_tableinfo.1.gz
/usr/share/man/man1/mysql_upgrade.1.gz
/usr/share/man/man1/mysqlaccess.1.gz
/usr/share/man/man1/mysql_waitpid.1.gz
/usr/share/man/man1/mysql_fix_extensions.1.gz
/usr/share/man/man1/mysqlman.1.gz
/usr/share/man/man1/mysqlbinlog.1.gz
/usr/share/man/man1/mysql_install_db.1.gz
/usr/share/man/man1/mysql_tzinfo_to_sql.1.gz
/usr/share/man/man1/mysql_secure_installation.1.gz
/usr/share/man/man1/mysqld_safe.1.gz
/usr/share/man/man1/mysqladmin.1.gz
/usr/share/man/man1/mysqlimport.1.gz
/usr/share/man/man1/mysql_zap.1.gz
/usr/share/man/man1/msql2mysql.1.gz
/usr/share/man/man1/mysqlshow.1.gz
/usr/share/man/man1/mysqldump.1.gz
/usr/share/man/man1/safe_mysqld.1.gz
/usr/share/man/man1/mysql_explain_log.1.gz
/usr/share/man/man1/mysql_config.1.gz
/usr/share/man/man1/mysqlbug.1.gz
/usr/share/man/man1/mysqld_multi.1.gz
/usr/share/man/man1/mysql_setpermission.1.gz
/usr/share/man/man1/mysqlhotcopy.1.gz
/usr/share/man/man1/mysql_find_rows.1.gz
/usr/share/man/man1/mysql_convert_table_format.1.gz
/usr/share/man/man1/mysql_fix_privilege_tables.1.gz
/usr/share/man/man1/mysqldumpslow.1.gz
/usr/share/man/man1/mysqltest.1.gz
/usr/share/man/man1/mysqlcheck.1.gz
/usr/share/man/man3/Bundle::DBD::mysql.3pm.gz
/usr/share/man/man3/DBD::mysql.3pm.gz
/usr/share/man/man3/DBD::mysql::INSTALL.3pm.gz
/usr/share/doc/mysql-server-5.0.77
/usr/share/doc/mysql-5.0.77
/usr/share/doc/selinux-policy-2.4.6/html/services_mysql.html
/usr/share/pixmaps/comps/mysql.png
/usr/share/info/mysql.info.gz
/usr/share/selinux/devel/include/services/mysql.if
/usr/bin/mysql_fix_extensions
/usr/bin/mysql
/usr/bin/mysqltestmanager
/usr/bin/mysqldumpslow
/usr/bin/mysql_upgrade_shell
/usr/bin/mysql_convert_table_format
/usr/bin/mysqlimport
/usr/bin/mysqldump
/usr/bin/mysqltestmanager-pwgen
/usr/bin/mysql_tzinfo_to_sql
/usr/bin/mysqlbug
/usr/bin/mysqlhotcopy
/usr/bin/mysqlaccess
/usr/bin/mysqltest
/usr/bin/mysqladmin
/usr/bin/mysql_upgrade
/usr/bin/mysqltestmanagerc
/usr/bin/mysqld_safe
/usr/bin/mysql_zap
/usr/bin/mysql_waitpid
/usr/bin/msql2mysql
/usr/bin/mysql_secure_installation
/usr/bin/mysql_fix_privilege_tables
/usr/bin/mysqlshow
/usr/bin/mysql_config
/usr/bin/mysql_setpermission
/usr/bin/mysql_tableinfo
/usr/bin/mysql_find_rows
/usr/bin/mysqld_multi
/usr/bin/mysqlcheck
/usr/bin/mysqlbinlog
/usr/bin/mysql_install_db
/usr/bin/mysql_explain_log
/usr/lib/mysql
/usr/lib/mysql/mysqlbug
/usr/lib/mysql/libmysqlclient_r.so.15.0.0
/usr/lib/mysql/libmysqlclient.so.15
/usr/lib/mysql/libmysqlclient_r.so.15
/usr/lib/mysql/mysql_config
/usr/lib/mysql/libmysqlclient.so.15.0.0
/usr/lib/python2.4/site-packages/sos/plugins/mysql.pyo
/usr/lib/python2.4/site-packages/sos/plugins/mysql.pyc
/usr/lib/python2.4/site-packages/sos/plugins/mysql.py
/var/log/mysqld.log
/var/run/mysqld
/var/run/mysqld/mysqld.pid
/var/lock/subsys/mysqld
/var/lib/mysql
/var/lib/mysql/mysql
/var/lib/mysql/mysql.sock
/root/.mysql_history
/selinux/booleans/mysqld_disable_trans
/selinux/booleans/allow_user_mysql_connect

Installing a LAMP stack on Oracle Enterprise Linux

After successfully installing MySQL on Oracle Enterprise Linux installing a LAMP (Linux/Apache/MySQL/PHP) stack can also be performed with a single command:

$ yum install -y httpd php php-mysql
# Start the Apache Httpd Process
$ /etc/init.d/httpd start

To test and confirm Apache Httpd and PHP, we can use the CLI browser lynx:

$ yum install -y lynx
$ echo "<? phpinfo() ?>" > /var/www/html/phpinfo.php
$ lynx http://localhost/phpinfo.php

If successful, you will find a web page that contains the following.

phpinfo() (p1 of 31)

   PHP Logo

PHP Version 5.1.6

   System Linux localhost.localdomain 2.6.18-164.el5 #1 SMP Thu Sep 3 04:15:13
   EDT 2009 x86_64
   Build Date Feb 11 2010 19:07:36
   Configure   Command   './configure'  '--build=x86_64-redhat-linux-gnu'
   '--host=x86_64-redhat-linux-gnu'    '--target=x86_64-redhat-linux-gnu'
   '--program-prefix=''--prefix=/usr''--exec-prefix=/usr''--bindir=/usr/bin'
   '--sbindir=/usr/sbin'    '--sysconfdir=/etc'    '--datadir=/usr/share'
   '--includedir=/usr/include'                      '--libdir=/usr/lib64'
   '--libexecdir=/usr/libexec'                     '--localstatedir=/var'
   '--sharedstatedir=/usr/com'                  '--mandir=/usr/share/man'
   '--infodir=/usr/share/info'             '--cache-file=../config.cache'
   '--with-libdir=lib64'                   '--with-config-file-path=/etc'

It is important to note that PHP is also a standalone scripting language that doesn’t require a web browser. You can use PHP on the command line, for example:

$ php --version
PHP 5.1.6 (cli) (built: Feb 11 2010 19:06:40)
Copyright (c) 1997-2006 The PHP Group
Zend Engine v2.1.0, Copyright (c) 1998-2006 Zend Technologies

$ echo "<?phpinfo()?>" | php | grep -i mysql
Configure Command =>  './configure' '--build=x86_64-redhat-linux-gnu' '--host=x86_64-redhat-linux-gnu' '--target=x86_64-redhat-linux-gnu' '--program-prefix=' '--prefix=/usr' '--exec-prefix=/usr' '--bindir=/usr/bin' '--sbindir=/usr/sbin' '--sysconfdir=/etc' '--datadir=/usr/share' '--includedir=/usr/include' '--libdir=/usr/lib64' '--libexecdir=/usr/libexec' '--localstatedir=/var' '--sharedstatedir=/usr/com' '--mandir=/usr/share/man' '--infodir=/usr/share/info' '--cache-file=../config.cache' '--with-libdir=lib64' '--with-config-file-path=/etc' '--with-config-file-scan-dir=/etc/php.d' '--disable-debug' '--with-pic' '--disable-rpath' '--without-pear' '--with-bz2' '--with-curl' '--with-exec-dir=/usr/bin' '--with-freetype-dir=/usr' '--with-png-dir=/usr' '--enable-gd-native-ttf' '--without-gdbm' '--with-gettext' '--with-gmp' '--with-iconv' '--with-jpeg-dir=/usr' '--with-openssl' '--with-png' '--with-pspell' '--with-expat-dir=/usr' '--with-pcre-regex=/usr' '--with-zlib' '--with-layout=GNU' '--enable-exif' '--enable-ftp' '--enable-magic-quotes' '--enable-sockets' '--enable-sysvsem' '--enable-sysvshm' '--enable-sysvmsg' '--enable-track-vars' '--enable-trans-sid' '--enable-yp' '--enable-wddx' '--with-kerberos' '--enable-ucd-snmp-hack' '--with-unixODBC=shared,/usr' '--enable-memory-limit' '--enable-shmop' '--enable-calendar' '--enable-dbx' '--enable-dio' '--with-mime-magic=/usr/share/file/magic.mime' '--without-sqlite' '--with-libxml-dir=/usr' '--with-xml' '--with-system-tzdata' '--enable-force-cgi-redirect' '--enable-pcntl' '--with-imap=shared' '--with-imap-ssl' '--enable-mbstring=shared' '--enable-mbstr-enc-trans' '--enable-mbregex' '--with-ncurses=shared' '--with-gd=shared' '--enable-bcmath=shared' '--enable-dba=shared' '--with-db4=/usr' '--with-xmlrpc=shared' '--with-ldap=shared' '--with-ldap-sasl' '--with-mysql=shared,/usr' '--with-mysqli=shared,/usr/lib64/mysql/mysql_config' '--enable-dom=shared' '--with-dom-xslt=/usr' '--with-dom-exslt=/usr' '--with-pgsql=shared' '--with-snmp=shared,/usr' '--enable-soap=shared' '--with-xsl=shared,/usr' '--enable-xmlreader=shared' '--enable-xmlwriter=shared' '--enable-fastcgi' '--enable-pdo=shared' '--with-pdo-odbc=shared,unixODBC,/usr' '--with-pdo-mysql=shared,/usr/lib64/mysql/mysql_config' '--with-pdo-pgsql=shared,/usr' '--with-pdo-sqlite=shared,/usr' '--enable-dbase=shared'
/etc/php.d/mysql.ini,
/etc/php.d/mysqli.ini,
/etc/php.d/pdo_mysql.ini,
mysql
MySQL Support => enabled
MYSQL_MODULE_TYPE => external
MYSQL_SOCKET => /var/lib/mysql/mysql.sock
MYSQL_INCLUDE => -I/usr/include/mysql
MYSQL_LIBS => -L/usr/lib64/mysql -lmysqlclient
mysql.allow_persistent => On => On
mysql.connect_timeout => 60 => 60
mysql.default_host => no value => no value
mysql.default_password => no value => no value
mysql.default_port => no value => no value
mysql.default_socket => no value => no value
mysql.default_user => no value => no value
mysql.max_links => Unlimited => Unlimited
mysql.max_persistent => Unlimited => Unlimited
mysql.trace_mode => Off => Off
mysqli
MysqlI Support => enabled
MYSQLI_SOCKET => /var/lib/mysql/mysql.sock
mysqli.default_host => no value => no value
mysqli.default_port => 3306 => 3306
mysqli.default_pw => no value => no value
mysqli.default_socket => no value => no value
mysqli.default_user => no value => no value
mysqli.max_links => Unlimited => Unlimited
mysqli.reconnect => Off => Off
PDO drivers => mysql, sqlite
pdo_mysql
PDO Driver for MySQL, client library version => 5.0.77

Short URL: rb42.com/oel-install-lamp

Installing MySQL on Oracle Enterprise Linux

One of the significant benefits of MySQL is it’s ease of use. Generally already installed on most Linux systems, MySQL can be installed by a single command if not yet present. On Oracle Enterprise Linux 5.4 you can use the following commands to check for MySQL, configure your yum repository and install MySQL.

# Check if already installed
$ rpm -qa | grep -i mysql

# Configure yum repository on new server
$ su -
$ cd /tmp
$ wget http://public-yum.oracle.com/public-yum-el5.repo
$ sed -e "s/enabled=0/enabled=1/" public-yum-el5.repo > /etc/yum.repos.d/public-yum-el5.repo

# Install MySQL
$ yum install -y mysql-server mysql

# Start and test MySQL Instance
$ /etc/init.d/mysqld start
$ mysql -uroot -e "SELECT VERSION()"

+-----------+
| VERSION() |
+-----------+
| 5.0.77    |
+-----------+

You can find more information about the Oracle public yum repository at http://public-yum.oracle.com You will also note that the version installed is 5.0. The current GA version of MySQL is 5.1, however Red Hat is notorious for taking time to update repositories more regularly. You can always use more current rpm files available at the MySQL downloads page.

If you want MySQL to be configured to automatically start and stop on your server you need to run the following command.

$ chkconfig mysqld on
$ chkconfig --list mysqld
mysqld          0:off   1:off   2:on    3:on    4:on    5:on    6:off

You can link to this post with the short url rb42.com/oel-install-mysql

Related Posts

Speaking at Oracle Open World 2010


I will be one of 18 MySQL speakers at Oracle Open World 2010 at the first ever MySQL Sunday. With a great diversity of technical, community and product talks this will be a great opportunity to get a cross section of MySQL content. Combined with Java One, this year’s Oracle Open World will include a lot more opportunity of technical and developer content then the more regular marketing material.

As the program chair for the first dedicated MySQL track at last month’s ODTUG Kaleidoscope 2010 our MySQL community now includes a larger number of target people. From the Oracle community come many highly technical and skilled resources, some with an understanding or appreciation of MySQL and many that are new to MySQL.

This is a great opportunity to share our knowledge and experience with MySQL.

References

Optimizing SQL Performance – The Art of Elimination

The most efficient performance optimization of a SQL statement is to eliminate it. Cary Millsap’s recent Kaleidoscope presentation again highlighted that improving performance is function of code path. Removing code will improve performance.

You may think that it could be hard to eliminate SQL, however when you know every SQL statement that is executed in your code path obvious improvements may be possible. In the sequence SQL was implemented sometimes easy observations can lead to great gains. Let me provide some actual client examples that were discovered by using the MySQL General Log.

Example 1

5 Query   SELECT *  FROM `artist`
5 Query   SELECT *  FROM `artist`
5 Query   SELECT *  FROM `artist`
5 Query   SELECT *  FROM `artist`
5 Query   SELECT *  FROM `artist`
5 Query   SELECT *  FROM `artist` WHERE (ArtistID = 196 )
5 Query   SELECT *  FROM `artist` WHERE (ArtistID = 2188 )
5 Query   SELECT *  FROM `artist`
5 Query   SELECT *  FROM `artist`
5 Query   SELECT *  FROM `artist`

In this example, the following was executed for a single page load. Not only did I find a bug where full-table scans occurred rather then being qualified, there were many repeating and unnecessary occurrences.

Example 2

SELECT option_name, option_value FROM wp_options WHERE autoload = 'yes'
SELECT option_value FROM wp_options WHERE option_name = 'aiosp_title_format' LIMIT 1
SELECT option_value FROM wp_options WHERE option_name = 'ec3_show_only_even' LIMIT 1
SELECT option_value FROM wp_options WHERE option_name = 'ec3_num_months' LIMIT 1
SELECT option_value FROM wp_options WHERE option_name = 'ec3_day_length' LIMIT 1
SELECT option_value FROM wp_options WHERE option_name = 'ec3_hide_event_box' LIMIT 1
SELECT option_value FROM wp_options WHERE option_name = 'ec3_advanced' LIMIT 1
SELECT option_value FROM wp_options WHERE option_name = 'ec3_navigation' LIMIT 1
SELECT option_value FROM wp_options WHERE option_name = 'ec3_disable_popups' LIMIT 1
SELECT option_value FROM wp_options WHERE option_name = 'sidebars_widgets' LIMIT 1

This is a stock WordPress installation and highlights a classic Row at a Time (RAT) processing.

Example 3

SELECT * FROM activities_theme WHERE theme_parent_id=0
SELECT * FROM activities_theme WHERE theme_parent_id=1
SELECT * FROM activities_theme WHERE theme_parent_id=2
SELECT * FROM activities_theme WHERE theme_parent_id=11
SELECT * FROM activities_theme WHERE theme_parent_id=16

In this client example, again RAT processing, I provided a code improvement to run these multiple queries in a single statement, otherwise known as Chunk At a Time (CAT) processing. It’s not rocket science however the elimination of the network component of several SQL statements can greatly reduce page load time.

SELECT *
FROM   activities_theme
WHERE  theme_parent_id in  (0,1,2,11,16) 

Example 4

The following represents one of the best improvement. During capture, the following query was executed 6,000 times over a 5 minute period. While you make think this is acceptable, the value passed wae 0. The pages_id is an auto_increment column which by definition does not have a 0 value. In this instance, a simple boundary condition in the code would eliminate this query.

SELECT pages_id, pages_livestats_code, pages_title,
       pages_parent, pages_exhibid, pages_theme,
       pages_accession_num
FROM pages WHERE pages_id = 0

There are many tips to improving and optimizing SQL. This is the simplest and often overlooked starting point.

Related articles include: The RAT and the CAT and We need more CAT’s

What do MySQL Consultants do?

One role of a MySQL consultant is to review an existing production system. Sometimes you have sufficient time and access, and other times you don’t. If I am given a limited time here is a general list of things I look at.

  1. Review Server architecture, OS, Memory, Disks (including raid and partition type), Network etc
  2. Review server load and identify physical bottleneck
  3. Look at all running processes
  4. Look specifically at MySQL processes
  5. Review MySQL Error Log
  6. Determine MySQL version
  7. Look at MySQL configuration (e.g. /etc/my.cnf)
  8. Look at running MySQL Variables
  9. Look at running MySQL status (x n times)
  10. Look at running MySQL INNODB status (x n times) if used
  11. Get Database and Schema Sizes
  12. Get Database Schema
  13. Review Slow Query Log
  14. Capture query sample via SHOW FULL PROCESSLIST (locked and long running)
  15. Analyze Binary Log file
  16. Capture all running SQL

Here are some of the commands I would run.

2. Review server load and identify physical bottleneck

$ vmstat 5 720 > vmstat.`date +%y%m%d.%H%M%S`.txt

4. Look at MySQL processes

$ ps -eopid,fname,rss,vsz,user,command | grep -e "RSS" -e "mysql"
  PID COMMAND    RSS    VSZ USER     COMMAND
 5463 grep       764   5204 ronald   grep -e RSS -e mysql
13894 mysqld_s   596   3936 root     /bin/sh /usr/bin/mysqld_safe
13933 mysqld   4787812 5127208 mysql /usr/sbin/mysqld --basedir=/usr --datadir=/vol/mysql/mysqldata --user=mysql --pid-file=/var/run/mysqld/mysqld.pid --skip-external-locking --port=3306 --socket=/var/run/mysqld/mysqld.sock
13934 logger     608   3840 root     logger -p daemon.err -t mysqld_safe -i -t mysqld

$ ps -eopid,fname,rss,vsz,user,command | grep " mysqld " | grep -v grep | awk '{print $3,$4}'
4787820 5127208

5. Review MySQL Error Log

The error log can be found in various different places based on the operating system and configuration. It is important to find the right log, the SHOW GLOBAL VARIABLES LIKE ‘log_error’ will determine the location.

This is generally overlooked, however this can quickly identify some underlying problems with a MySQL environment.

7. Look at MySQL configuration

$ [ -f /etc/my.cnf ] &&  cat /etc/my.cnf
$ [ -f /etc/mysql/my.cnf ] &&  cat /etc/mysql/my.cnf
$ find / -name  "*my*cnf" 2>/dev/null

8. Look at running MySQL Variables

$ mysqladmin -uroot -p variables

9. Look at running MySQL status (x n times)

$ mysqladmin -uroot -p extended-status

It is important to run this several times at regular intervals, say 60 seconds, 60 minutes, or 24 hours.

I also have dedicated scripts that can perform this. Check out Log MySQL Stats.

11. Get Database and Schema Sizes

Check out my scripts on my MySQL DBA page

14. Capture Locked statements

Check out my script for Capturing MySQL sessions.

15. Analyze Binary Log file

Check out my post on using mk-query-digest.

16. Capture all SQL

Check out my post on DML Stats per table

Moving forward

Of course the commands I run exceeds this initial list, and gathering this information is only

Timing your SQL queries

When working interactively with the MySQL client, you receive feedback of the time the query took to complete to a granularity of 10 ms.

Enabling profiling is a simple way to get more a more accurate timing of running queries. In the following example you can see the time the kernel took to run an explain, the query, and alter, and repeat explain and query.

mysql> set profiling=1;
mysql> EXPLAIN SELECT ...
mysql> SELECT ...
mysql> ALTER ...
mysql> show profiles;
+----------+------------+-------------------------
| Query_ID | Duration   | Query
+----------+------------+-------------------------
|        1 | 0.00036500 | EXPLAIN SELECT sbvi.id a
|        2 | 0.00432700 | SELECT sbvi.id as sbvi_i
|        3 | 2.83206100 | alter table sbvi drop in
|        4 | 0.00047500 | explain SELECT sbvi.id a
|        5 | 0.00367100 | SELECT sbvi.id as sbvi_i
+----------+------------+-------------------------

More information at Show Profiles documentation page.

Getting started with Ruby and Sinatra

I’ve been doing a little work with Ruby, starting with some XHTML parsing with Nokogiri. I’ve just created my first web page using Sinatra.

While the instructions makes it look simple, it was a little more complex due a package dependency error.

Installation

$ sudo gem install sinatra
Password:
Successfully installed rack-1.2.1
Successfully installed sinatra-1.0
2 gems installed
Installing ri documentation for rack-1.2.1...
Installing ri documentation for sinatra-1.0...
Installing RDoc documentation for rack-1.2.1...
Installing RDoc documentation for sinatra-1.0...

Smoking it

Following the 5 line example on the home page, didn’t produce the result I expected.

 ruby rb42.rb
/Library/Ruby/Gems/1.8/gems/rack-1.2.1/lib/rack/utils.rb:138:in `union': can't convert Array into String (TypeError)
	from /Library/Ruby/Gems/1.8/gems/rack-1.2.1/lib/rack/utils.rb:138
	from /Library/Ruby/Site/1.8/rubygems/custom_require.rb:31:in `gem_original_require'
	from /Library/Ruby/Site/1.8/rubygems/custom_require.rb:31:in `require'
	from /Library/Ruby/Gems/1.8/gems/rack-1.2.1/lib/rack/request.rb:1
	from /Library/Ruby/Site/1.8/rubygems/custom_require.rb:31:in `gem_original_require'
	from /Library/Ruby/Site/1.8/rubygems/custom_require.rb:31:in `require'
	from /Library/Ruby/Gems/1.8/gems/rack-1.2.1/lib/rack/showexceptions.rb:3
	from /Library/Ruby/Site/1.8/rubygems/custom_require.rb:31:in `gem_original_require'
	 ... 7 levels...
	from /Library/Ruby/Gems/1.8/gems/sinatra-1.0/lib/sinatra.rb:4
	from /Library/Ruby/Site/1.8/rubygems/custom_require.rb:36:in `gem_original_require'
	from /Library/Ruby/Site/1.8/rubygems/custom_require.rb:36:in `require'
	from rb42.rb:2

Some Googling found a reference to a compatibility problem. While the syntax given on the post wasn’t correct, it was sufficient for me to find a correct solution.

$  sudo gem uninstall rack
Remove executables:
	rackup

in addition to the gem? [Yn]  y
Removing rackup

You have requested to uninstall the gem:
	rack-1.2.1
sinatra-1.0 depends on [rack (>= 1.0)]
If you remove this gems, one or more dependencies will not be met.
Continue with Uninstall? [Yn]  y
Successfully uninstalled rack-1.2.1

$ sudo gem install rack --version '1.2.0'
Successfully installed rack-1.2.0
1 gem installed
Installing ri documentation for rack-1.2.0...
Installing RDoc documentation for rack-1.2.0...

And now expected results starting then viewing http://localhost:4567/

$ ruby rb42.rb
== Sinatra/1.0 has taken the stage on 4567 for development with backup from Mongrel

Environment

$ sw_vers
ProductName:	Mac OS X
ProductVersion:	10.5.8
BuildVersion:	9L31a
$ ruby --version
ruby 1.8.6 (2009-06-08 patchlevel 369) [universal-darwin9.0]
$ gem --version
1.3.6

Upcoming Conferences with dedicated MySQL content

We recently held a dedicated MySQL Track at ODTUG Kaleidoscope 2010 conference for 4 days. This is the first of many Oracle events that will begin to include dedicated MySQL content.

If your attending OSCON 2010 in the next few weeks you will see a number of MySQL presentations.

MySQL will be represented at Open World 2010 in September with MySQL Sunday. Giuseppe has created a great one page summary of speakers. This event is described as technical sessions, an un-conference and an fireside chat with Edward Screven. I’ve seen tickets listed at $50 or $75 for the day.

Open SQL Camp will be held in Germany in August, and Boston in October. This is a great FREE event that includes technical content not just on MySQL but other open source databases and data stores.

You will also find dedicated MySQL tracks in Europe at the German Oracle Users Group (DOAG) conference in November and the United Kingdom Oracle Users Group (UKOUG) in November that I am planning on attending.

In 2011 there is already a lineup of events that will all contain multiple tracks of MySQL content.

For the MySQL community the introduction of various large Oracle conferences may be confusing. From my perspective I describe the big three as.

  • Oracle Open World is targeted towards marketing. This includes product announcements, case studies and first class events.
  • Collaborate is targeted towards deployment and includes 3 different user groups, the IOUG representing the Oracle Database, the Oracle Applications User Group, and the Quest Group.
  • ODTUG Kaleidoscope is targeted towards development. This includes the tools and technologies for developers and DBA’s to do your job.

Having just attended Kaleidoscope 2010, and being a relative unknown I left with a great impression of an open, technical and welcoming event. There was a great atmosphere, great events with excellent food for breakfast, lunch and dinner and I now have a long list of new friends. This conference very much reflected being part of a greater extended family, the experience I have enjoyed at previous MySQL conferences. I’ve already committed to being involved next year.

Improving MySQL Productivity – From Design to Implementation

My closing presentation at the dedicated MySQL track at ODTUG Kaleidoscope 2010 discussed various techniques and best practices for improving the ROI of developer resources using MySQL. Included in the sections on Design, Security, Development, Testing, Implementation, Instrumentation and Support were also a number of horror stories of not what to do, combined with practical examples of improving productivity.

MySQL Idiosyncrasies That Bite

The following are my slides that I presented at ODTUG Kaleidoscope 2010. This presentation talks about the MySQL defaults including a non-transactional state, silent data truncations, date management, and transaction isolation options. These are all critical for data integrity and consistency. I also cover in-depth topics including SQL_MODE, character sets and collations.

Getting Nokogiri working under Mac OS X

The official Installation documentation states:

sudo port install libxml2 libxslt
sudo gem install nokogiri

however I found this not to work for me. The following did work.

$ sudo port install libxml2 libxslt

$ sudo gem install nokogiri
ERROR:  could not find nokogiri locally or in a repository

$ sudo gem sources -a http://gems.github.com
Bulk updating Gem source index for: http://gems.github.com
Updating metadata for 1 gems from http://gems.rubyforge.org

$ sudo gem install nokogiri
ERROR:  could not find nokogiri locally or in a repository

$ sudo gem update --system
Updating RubyGems...
Attempting remote update of rubygems-update
Successfully installed rubygems-update-1.3.6
1 gem installed
Installing ri documentation for rubygems-update-1.3.6...
Installing RDoc documentation for rubygems-update-1.3.6...
Updating version of RubyGems to 1.3.6
Installing RubyGems 1.3.6
RubyGems 1.3.6 installed

$ sudo gem install nokogiri
Building native extensions.  This could take a while...
Successfully installed nokogiri-1.4.2
1 gem installed
Installing ri documentation for nokogiri-1.4.2...
No definition for parse_memory
No definition for parse_file
No definition for parse_with
No definition for get_options
No definition for set_options
Installing RDoc documentation for nokogiri-1.4.2...
No definition for parse_memory
No definition for parse_file
No definition for parse_with
No definition for get_options
No definition for set_options

I’m not sure why I got those additional errors, however I was able to confirm a valid installation with.

$ irb
>> require ‘nokogiri’
=> true
>> quit

Still room at Kaleidoscope for MySQL attendees

Today I received notice that next week’s Velocity conference is at maximum capacity. With just under 2 weeks before the start of ODTUG Kaleidoscope in Washington DC we still have room for late registrations. There is 4 days of MySQL content, free events and also a Sunday Symposium that includes talks on performance and high availability.

Contact any of the MySQL speakers directly and you can receive a special 50% discount code. This is only for MySQL attendees.

If you live in the DC area and only want the FREE option then come along and join use on Monday night for a free session and reception.

ODTUG Kaleidoscope 2010
July 27 – July 1
Marriott Wardman Part Hotel
2660 Woodley Road NW
Washington, District Of Columbia 20008
www.odtugkaleidoscope.com

Conference highlights include

Community Service Day – Saturday, June 26, 8:00 a.m. – 1:00 p.m.
Join ODTUG volunteers and help refurbish a school in D.C.  Under the guidance of Greater DC Cares (GDCC), the leading and largest nonprofit coordinator of volunteerism in the D.C. region, ODTUGgers will: Sort books, beautify school grounds, and paint games on blacktop outside of hte school.

There is still time to sign up!  

Four Full-day Symposia – Sunday, June 27, 8:30 a.m. – 4:00 p.m.
Application Express; Oracle EPM and Essbase; Security, Scalability, and Performance; SOA and BPM. One-day registration available.

Welcome Reception/Battle of the Rock Bands – Sunday, June 27, 6:15 – 8:00 p.m.
Meet the exhibitors and compete in the “Battle of the Rock Bands.” Sign up to play.


Opening General Session – Monday, June 28, 8:30 – 10:00 a.m.
Awards for Best Technical Paper and Best 2009 Presentations
Keynote – “Future of the Internet and its Social Impact” by Lee Rainie, Director of the PEW Research Center’s Internet & American Life Project.
Sundown Sessions with Oracle ACE Directors – Monday, June 28, 5:45 – 6:45 p.m.
Reception to meet the Oracle ACE Directors immediately follows – 6:45 – 7:45 p.m.

Special Event – Wednesday, June 30, 6:30 – 10:00 p.m.
Featuring comedian John Heffron, 2nd season champion of the hit TV show, Last Comic Standing.
Music by live cover band, Right Foot Red

MongoDB Experience: Server logging

By default the mongod process sends all output to stdout. You can also specify the daemon to log to file which is necessary for any production implementation. For example:

$ mongod --logpath=`pwd`/mongo.log  &
all output going to: /home/rbradfor/projects/mongo/mongo.log
^C

As you can see there is still a message to stdout, that should be cleaned up for a GA release. The output you will see for a clean startup/shutdown is:

Fri Jun 11 14:05:29 Mongo DB : starting : pid = 7990 port = 27017 dbpath = /home/rbradfor/projects/mongo/data/cu
rrent master = 0 slave = 0  64-bit
Fri Jun 11 14:05:29 db version v1.4.3, pdfile version 4.5
Fri Jun 11 14:05:29 git version: 47ffbdfd53f46edeb6ff54bbb734783db7abc8ca
Fri Jun 11 14:05:29 sys info: Linux domU-12-31-39-06-79-A1 2.6.21.7-2.ec2.v1.2.fc8xen #1 SMP Fri Nov 20 17:48:28
 EST 2009 x86_64 BOOST_LIB_VERSION=1_41
Fri Jun 11 14:05:29 waiting for connections on port 27017
Fri Jun 11 14:05:29 web admin interface listening on port 28017
Fri Jun 11 14:05:31 got kill or ctrl c signal 2 (Interrupt), will terminate after current cmd ends
Fri Jun 11 14:05:31 now exiting
Fri Jun 11 14:05:31  dbexit:
Fri Jun 11 14:05:31 	 shutdown: going to close listening sockets...
Fri Jun 11 14:05:31 	 going to close listening socket: 5
Fri Jun 11 14:05:31 	 going to close listening socket: 6
Fri Jun 11 14:05:31 	 shutdown: going to flush oplog...
Fri Jun 11 14:05:31 	 shutdown: going to close sockets...
Fri Jun 11 14:05:31 	 shutdown: waiting for fs preallocator...
Fri Jun 11 14:05:31 	 shutdown: closing all files...
Fri Jun 11 14:05:31      closeAllFiles() finished
Fri Jun 11 14:05:31 	 shutdown: removing fs lock...
Fri Jun 11 14:05:31  dbexit: really exiting now

MongoDB logging does not give an option to format the date/time appropriately. The format does not match the syslog of Ubuntu/CentOS

Jun  9 10:05:46 barney kernel: [1025968.983209] SGI XFS with ACLs, security attributes, realtime, large block/in
ode numbers, no debug enabled
Jun  9 10:05:46 barney kernel: [1025968.984518] SGI XFS Quota Management subsystem
Jun  9 10:05:46 barney kernel: [1025968.990183] JFS: nTxBlock = 8192, nTxLock = 65536
Jun  9 10:05:46 barney kernel: [1025969.007624] NTFS driver 2.1.29 [Flags: R/O MODULE].
Jun  9 10:05:46 barney kernel: [1025969.020995] QNX4 filesystem 0.2.3 registered.
Jun  9 10:05:46 barney kernel: [1025969.039264] Btrfs loaded
Jun  8 00:00:00 dc1 nagios: CURRENT HOST STATE: localhost;UP;HARD;1;PING OK - Packet loss = 0%, RTA = 0.01 ms
Jun  8 00:00:00 dc1 nagios: CURRENT SERVICE STATE: localhost;Current Load;OK;HARD;1;OK - load average: 0.00, 0.00, 0.00
Jun  8 00:00:00 dc1 nagios: CURRENT SERVICE STATE: localhost;Current Users;OK;HARD;1;USERS OK - 2 users currently logged in
Jun  8 00:00:00 dc1 nagios: CURRENT SERVICE STATE: localhost;HTTP;CRITICAL;HARD;4;Connection refused
Jun  8 00:00:00 dc1 nagios: CURRENT SERVICE STATE: localhost;PING;OK;HARD;1;PING OK - Packet loss = 0%, RTA = 0.01 ms
Jun  8 00:00:00 dc1 nagios: CURRENT SERVICE STATE: localhost;Root Partition;OK;HARD;1;DISK OK - free space: / 107259 MB (49% inode=98%):
Jun  8 00:00:00 dc1 nagios: CURRENT SERVICE STATE: localhost;SSH;OK;HARD;1;SSH OK - OpenSSH_4.3 (protocol 2.0)

And for reference here is the mysql format, which is also not configurable.

100605 16:43:38 mysqld_safe Starting mysqld daemon with databases from /opt/mysql51/data
100605 16:43:38 [Warning] '--log_slow_queries' is deprecated and will be removed in a future release. Please use ''--slow_query_log'/'--slow_query_log_fi
le'' instead.
100605 16:43:38 [Warning] '--log' is deprecated and will be removed in a future release. Please use ''--general_log'/'--general_log_file'' instead.
100605 16:43:38 [Warning] No argument was provided to --log-bin, and --log-bin-index was not used; so replication may break when this MySQL server acts a
s a master and has his hostname changed!! Please use '--log-bin=dc1-bin' to avoid this problem.
/opt/mysql51/bin/mysqld: File './dc1-bin.index' not found (Errcode: 13)
100605 16:43:38 [ERROR] Aborting

However unlike other products including MySQL the next execution of the mongod process overwrites the log file. This will catch some administrators out. You need to remember to also add –logappend. Personally I’d prefer to see this is the default

$ mongod --logpath=`pwd`/mongo.log --logappend

I did observe some confusion on messaging. Using the mongo shell you get a jumble of logging messages during a shutdown.

$ mongo
MongoDB shell version: 1.4.3
url: test
connecting to: test
type "help" for help
> use admin
switched to db admin
> db.shutdownServer();
Fri Jun 11 13:54:08 query failed : admin.$cmd { shutdown: 1.0 } to: 127.0.0.1
server should be down...
Fri Jun 11 13:54:08 trying reconnect to 127.0.0.1
Fri Jun 11 13:54:08 reconnect 127.0.0.1 ok
Fri Jun 11 13:54:08 query failed : admin.$cmd { getlasterror: 1.0 } to: 127.0.0.1
Fri Jun 11 13:54:08 JS Error: Error: error doing query: failed (anon):1284
> exit
bye

This also results in an unformatted message in the log file for some reason.

$ tail mongo.log
Fri Jun 11 13:54:08 	 shutdown: removing fs lock...
Fri Jun 11 13:54:08  dbexit: really exiting now
Fri Jun 11 13:54:08 got request after shutdown()
ERROR: Client::~Client _context should be NULL: conn

Nothing of any critical nature however all important for system administrators that have monitoring scripts or using monitoring products.

MongoDB Experience: Key/Value Store

MongoDB is categorized as a schema-less, schema-free or a document orientated data store. Another category of NoSQL product is the key/value store. It had not dawned on me until a discussion with some of the 10gen employees that MongoDB is also a key/value store, this is just a subset of features.

How would you consider the design of a key/value store? Using the memached model, there are 4 primary attributes to consider:

  • The Key to store/retrieve
  • The Value for the given key
  • An auto expiry of the cached data
  • A key scope enabling multiple namespaces

There are three primary functions:

  • Put a given Key/Value pair
  • Get a given Key
  • Delete a given Key

Let’s explore the options. The first is to create a new collection for each key. That way there is only one row per key,

> use keystore
> var d = new Date();
> var id = "key1";
> var kv = { key: id,val: "Hello World",expires: d}
> db.key1.save(kv);
> db.key1.find();
{ "_id" : ObjectId("4c126095c68fcaf3b0e07a2b"), "key" : "key1", "val" : "Hello World", "expires" : "Fri Jun 11 2010 12:09:51 GMT-0400 (EDT)" }

However when we start loading we run into a problem.

> db.key99999.save({key: "key99999", val: "Hello World", expires: new Date()})
too many namespaces/collections
> show collections;
Fri Jun 11 12:49:02 JS Error: uncaught exception: error: {
	"$err" : "too much key data for sort() with no index.  add an index or specify a smaller limit"
}
> db.stats()
{
	"collections" : 13661,
	"objects" : 26118,
	"dataSize" : 2479352,
	"storageSize" : 93138688,
	"numExtents" : 13665,
	"indexes" : 13053,
	"indexSize" : 106930176,
	"ok" : 1
}

I did read there was a limit on the number of collections at Using a Large Number of Collections.
Also for reference, I look at the underlying data files shows the ^2 increment of data files.

$ ls -lh data/current
total 2.2G
-rw------- 1 rbradfor rbradfor  64M 2010-06-11 12:45 keystore.0
-rw------- 1 rbradfor rbradfor 128M 2010-06-11 12:45 keystore.1
-rw------- 1 rbradfor rbradfor 256M 2010-06-11 12:46 keystore.2
-rw------- 1 rbradfor rbradfor 512M 2010-06-11 12:48 keystore.3
-rw------- 1 rbradfor rbradfor 1.0G 2010-06-11 12:48 keystore.4
-rw------- 1 rbradfor rbradfor  16M 2010-06-11 12:48 keystore.ns
> db.dropDatabase();
{ "dropped" : "keystore.$cmd", "ok" : 1 }

In my next test I’ll repeat by adding the key as a row or document for just one collection.

MongoDB Experience: Stats Example App

The best way to learn any new product is to a) read the manual, and b) start using the product.

I created a simple sample application so I could understand the various functions including adding data, searching as well as management functions etc. As with any good sample application using a source of data that already exists always makes life easier. For this example I’m going to use the Operating System output so I will have an ever increasing amount of output for no additional work.

I will be starting with a database called ‘stats’. For this database my first collection is going to be called ‘system’ and this is going to record the most basic of information including date/time, host and cpu (user,sys,idle) stats. I have a simple shell script that creates an appropriate JSON string and I use mongoimport to load the data. Here is my Version 0.1 architectural structure.

mongo> use stats;
mongo> db.system.findOne();
{
	"_id" : ObjectId("4c11183580399ad2db4f503b"),
	"host" : "barney",
	"epoch" : 1276188725,
	"date" : "Thu Jun 10 12:52:05 EDT 2010",
	"cpu" : {
		"user" : 2,
		"sys" : 2,
		"idle" : 95
	},
	"raw" : " 11435699 1379565 9072198 423130352 2024835 238766 2938641 0 0"
}

I made some initial design decisions before I understand the full strengths/limitation of MongoDB as well as what my actual access paths to data will be.
While I’m using a seconds since epoch for simple range searching, I’m adding a presentation date for user readability. I’ve created a different sub element for cpu, because it a) this element has a number of individual attributes I will want to report and search on, and b) this collection should be extended to include other information like load average, running processes, memory etc.

If my shell script runs in debug mode, I also record the raw data used to determine the end result. This makes debugging easier.

Here is my first query.

Find all statistics between two dates. It took a bit of getting the correct construct syntax correct, $le and $ge didn’t work so RTFM highlighted the correct syntax. I also first included elements for epoch, which resulted in a OR condition, I see you can add multiple comparison operators to a single element to get an AND operation.

mongo> db.system.find({epoch: { $gte: 1276188725, $lte: 1276188754}});
{ "_id" : ObjectId("4c11183580399ad2db4f503b"), "host" : "barney", "epoch" : 1276188725, "date" : "Thu Jun 10 12:52:05 EDT 2010", "cpu" : { "user" : 2, "sys" : 2, "idle" : 95 }, "raw" : " 11435699 1379565 9072198 423130352 2024835 238766 2938641 0 0" }
{ "_id" : ObjectId("4c11184c80399ad2db4f503c"), "host" : "barney", "epoch" : 1276188748, "date" : "Thu Jun 10 12:52:28 EDT 2010", "cpu" : { "user" : 2, "sys" : 2, "idle" : 95 }, "raw" : " 11436605 1379565 9072320 423138450 2024862 238770 2938641 0 0" }
{ "_id" : ObjectId("4c11185080399ad2db4f503d"), "host" : "barney", "epoch" : 1276188752, "date" : "Thu Jun 10 12:52:32 EDT 2010", "cpu" : { "user" : 2, "sys" : 2, "idle" : 95 }, "raw" : " 11437005 1379565 9072330 423139527 2024862 238770 2938641 0 0" }
{ "_id" : ObjectId("4c11185180399ad2db4f503e"), "host" : "barney", "epoch" : 1276188753, "date" : "Thu Jun 10 12:52:33 EDT 2010", "cpu" : { "user" : 2, "sys" : 2, "idle" : 95 }, "raw" : " 11437130 1379565 9072334 423139862 2024862 238770 2938641 0 0" }
{ "_id" : ObjectId("4c11185280399ad2db4f503f"), "host" : "barney", "epoch" : 1276188754, "date" : "Thu Jun 10 12:52:34 EDT 2010", "cpu" : { "user" : 2, "sys" : 2, "idle" : 95 }, "raw" : " 11437316 1379565 9072338 423140325 2024910 238770 2938641 0 0" }

Assuming I’m going to have stats from more then one server in my data, we should always filter by hostname, and then for given period.

mongo> db.system.find({host: "barney", epoch: { $gte: 1276188725, $lte: 1276188754}});

If I only want to see the Date/Time and CPU stats, I can show a subset of the elements found.

mongo> db.system.find({epoch: { $gte: 1276188725, $lte: 1276188754}}, {date:1,cpu:1});
{ "_id" : ObjectId("4c11183580399ad2db4f503b"), "date" : "Thu Jun 10 12:52:05 EDT 2010", "cpu" : { "user" : 2, "sys" : 2, "idle" : 95 } }
{ "_id" : ObjectId("4c11184c80399ad2db4f503c"), "date" : "Thu Jun 10 12:52:28 EDT 2010", "cpu" : { "user" : 2, "sys" : 2, "idle" : 95 } }
...

Filtering on a sub-element is also possible however I found that the representation of strings and numbers does not do an implied conversion. In the following example “2” does not match any results, while 2 does.

mongo> db.system.findOne({host: "barney", "cpu.user": "2"})
null


mongo> db.system.findOne({host: "barney", "cpu.user": 2})
{
	"_id" : ObjectId("4c11161680399ad2db4f5033"),
	"host" : "barney",
	"epoch" : 1276188182,
	"date" : "Thu Jun 10 12:43:02 EDT 2010",
	"cpu" : {
		"user" : 2,
		"sys" : 2,
		"idle" : 95
	}
}

Given the collection and load process works, data is being recorded and I can perform some searching I now have the basis for adding additional rich data elements, learning about the internal DBA operations possible after I fix the bug with all my values being 2/2/95.

MongoDB Experience: Replication 101

After successfully installing and testing mongoDB it’s very easy to create a replication environment.

$ mkdir -p data/{master,slave}
$ mongod --dbpath=`pwd`/data/master --master --port 28011 > master.log 2>&1 &
# Always check your log file
$ cat master.log
$ mongod --dbpath=`pwd`/data/slave --slave --source localhost:28011 --port 28022 > slave.log 2>&1 &
$ cat slave.log

The options are relatively descriptive and straightforward.

  • –dbpath – The directory for data (we set because we are running master/slave on same server)
  • –port – Likewise we are running multiple instances on same machine
  • –master – I’m the master
  • –slave – I’m a slave
  • –source – For slaves, tell them were the source (i.e. master is)

What I found under the covers was a difference from the single instance version. There is a series of ‘local’ files for the namespace, where in the single instance version there were ‘test’ files.

$ ls -ltR data
total 0
drwxr-xr-x  6 rbradfor  staff  204 Jun 10 10:24 slave
drwxr-xr-x  5 rbradfor  staff  170 Jun 10 10:22 master

data/slave:
total 163848
drwxr-xr-x  2 rbradfor  staff        68 Jun 10 10:24 _tmp
-rw-------  1 rbradfor  staff  67108864 Jun 10 10:24 local.0
-rw-------  1 rbradfor  staff  16777216 Jun 10 10:24 local.ns
-rwxr-xr-x  1 rbradfor  staff         6 Jun 10 10:24 mongod.lock

data/slave/_tmp:

data/master:
total 163848
-rw-------  1 rbradfor  staff  67108864 Jun 10 10:22 local.0
-rw-------  1 rbradfor  staff  16777216 Jun 10 10:22 local.ns
-rwxr-xr-x  1 rbradfor  staff         6 Jun 10 10:22 mongod.lock

A quick replication test.

$ mongo --port 28011
MongoDB shell version: 1.4.3
url: test
connecting to: 127.0.0.1:28011/test
type "help" for help
> db.foo.save({s:"Hello world"});
> db.foo.find();
{ "_id" : ObjectId("4c10f7904a30c35548b0af06"), "s" : "Hello world" }
> exit
bye

$ mongo --port 28022
MongoDB shell version: 1.4.3
url: test
connecting to: 127.0.0.1:28022/test
type "help" for help
> db.foo.find();
{ "_id" : ObjectId("4c10f7904a30c35548b0af06"), "s" : "Hello world" }
> exit

A look now at the underlying data shows a ‘test’ namespace which confirms the lazy instantiation approach. The ‘local’ namespace files are obviously a reflection of the –master/–slave operation.

$ ls -ltR data
total 0
drwxr-xr-x  9 rbradfor  staff  306 Jun 10 10:32 slave
drwxr-xr-x  8 rbradfor  staff  272 Jun 10 10:32 master

data/slave:
total 589832
-rw-------  1 rbradfor  staff  134217728 Jun 10 10:33 test.1
drwxr-xr-x  2 rbradfor  staff         68 Jun 10 10:32 _tmp
-rw-------  1 rbradfor  staff   67108864 Jun 10 10:32 test.0
-rw-------  1 rbradfor  staff   16777216 Jun 10 10:32 test.ns
-rw-------  1 rbradfor  staff   67108864 Jun 10 10:24 local.0
-rw-------  1 rbradfor  staff   16777216 Jun 10 10:24 local.ns
-rwxr-xr-x  1 rbradfor  staff          6 Jun 10 10:24 mongod.lock

data/master:
total 327688
drwxr-xr-x  2 rbradfor  staff        68 Jun 10 10:32 _tmp
-rw-------  1 rbradfor  staff  67108864 Jun 10 10:32 test.0
-rw-------  1 rbradfor  staff  16777216 Jun 10 10:32 test.ns
-rw-------  1 rbradfor  staff  67108864 Jun 10 10:22 local.0
-rw-------  1 rbradfor  staff  16777216 Jun 10 10:22 local.ns
-rwxr-xr-x  1 rbradfor  staff         6 Jun 10 10:22 mongod.lock

By default there appears to be no read-only default state for a slave. I was able to add new data to the slave.

$ mongo --port 28022
MongoDB shell version: 1.4.3
url: test
connecting to: 127.0.0.1:28022/test
type "help" for help
> db.foo.save({s:"Hello New York"});
> db.foo.find();
{ "_id" : ObjectId("4c10f7904a30c35548b0af06"), "s" : "Hello world" }
{ "_id" : ObjectId("4c10f864d8e80f1a1ad305cf"), "s" : "Hello New York" }
>

A closer look at this ‘local’ namespace and a check via the docs gives us details of the slave configuration.

$ mongo --port 28022
MongoDB shell version: 1.4.3
url: test
connecting to: 127.0.0.1:28022/test
type "help" for help
> show dbs;
admin
local
test
> use local;
switched to db local
> show collections;
oplog.$main
pair.sync
sources
system.indexes
> db.sources.find();
{ "_id" : ObjectId("4c10f5b633308f7c3d7afc45"), "host" : "localhost:28011", "source" : "main", "syncedTo" : { "t" : 1276180895000, "i" : 1 }, "localLogTs" : { "t" : 1276180898000, "i" : 1 } }

You can also with the mongo client connect directly to a collection via the command line.

$ mongo localhost:28022/local
MongoDB shell version: 1.4.3
url: localhost:28022/local
connecting to: localhost:28022/local
type "help" for help
> db.sources.find();
{ "_id" : ObjectId("4c10f5b633308f7c3d7afc45"), "host" : "localhost:28011", "source" : "main", "syncedTo" : { "t" : 1276180775000, "i" : 1 }, "localLogTs" : { "t" : 1276180778000, "i" : 1 } }
> exit
bye

The shell gives 3 convenience commands for showing replication state.

On the Slave

$ mongo --port 28022
> db.getReplicationInfo();
{
	"logSizeMB" : 50,
	"timeDiff" : 1444,
	"timeDiffHours" : 0.4,
	"tFirst" : "Thu Jun 10 2010 10:24:54 GMT-0400 (EDT)",
	"tLast" : "Thu Jun 10 2010 10:48:58 GMT-0400 (EDT)",
	"now" : "Thu Jun 10 2010 10:48:59 GMT-0400 (EDT)"
}
> db.printReplicationInfo();
configured oplog size:   50MB
log length start to end: 1444secs (0.4hrs)
oplog first event time:  Thu Jun 10 2010 10:24:54 GMT-0400 (EDT)
oplog last event time:   Thu Jun 10 2010 10:48:58 GMT-0400 (EDT)
now:                     Thu Jun 10 2010 10:49:07 GMT-0400 (EDT)
> db.printSlaveReplicationInfo();
source:   localhost:28011
syncedTo: Thu Jun 10 2010 10:49:25 GMT-0400 (EDT)
          = 1secs ago (0hrs)

On the master, the same commands are applicable, output basically the same.

$ mongo --port 28011
> db.getReplicationInfo();
{
	"logSizeMB" : 50,
	"timeDiff" : 1714,
	"timeDiffHours" : 0.48,
	"tFirst" : "Thu Jun 10 2010 10:22:01 GMT-0400 (EDT)",
	"tLast" : "Thu Jun 10 2010 10:50:35 GMT-0400 (EDT)",
	"now" : "Thu Jun 10 2010 10:50:40 GMT-0400 (EDT)"
}
> db.printReplicationInfo();
configured oplog size:   50MB
log length start to end: 1714secs (0.48hrs)
oplog first event time:  Thu Jun 10 2010 10:22:01 GMT-0400 (EDT)
oplog last event time:   Thu Jun 10 2010 10:50:35 GMT-0400 (EDT)
now:                     Thu Jun 10 2010 10:50:45 GMT-0400 (EDT)
> db.printSlaveReplicationInfo();
local.sources is empty; is this db a --slave?
>

From these commands there seems no obvious way to easily identify if an instance is a master or not.

References

DBA operations from shell
Replication
Master/Slave Replication

MongoDB Experience: Gotcha with collection names

In my earlier tests I bulk loaded data with the following command.

mongoimport -d olympics -c olympic_event -type tsv --headerline -f name,id,sport,demonstration_competitions,olympic_games_contested,competitions,contested_as_demonstration_event --drop olympic_event.tsv
connected to: 127.0.0.1
dropping: olympics.olympic_event
imported 775 objects

As you can see I imported 775 objects, however when I went to review them via the mongo interactive shell I found no data.

> use olympics;
switched to db olympics
> db.olypics.olympic_event.find();
# No results?

I was able to confirm these objects were in the namespace.

> db.system.namespaces.find();
{ "name" : "olympics.system.indexes" }
{ "name" : "olympics.demonstration_event_athlete_relationship" }
{ "name" : "olympics.demonstration_event_athlete_relationship.$_id_" }
{ "name" : "olympics.olympic_athlete" }
{ "name" : "olympics.olympic_athlete.$_id_" }
{ "name" : "olympics.olympic_athlete_affiliation" }
{ "name" : "olympics.olympic_athlete_affiliation.$_id_" }
{ "name" : "olympics.olympic_bidding_city" }
{ "name" : "olympics.olympic_bidding_city.$_id_" }
{ "name" : "olympics.olympic_city_bid" }
{ "name" : "olympics.olympic_city_bid.$_id_" }
{ "name" : "olympics.olympic_demonstration_competition" }
{ "name" : "olympics.olympic_demonstration_competition.$_id_" }
{ "name" : "olympics.olympic_demonstration_medal_honor" }
{ "name" : "olympics.olympic_demonstration_medal_honor.$_id_" }
{ "name" : "olympics.olympic_event" }
{ "name" : "olympics.olympic_event.$_id_" }
{ "name" : "olympics.olympic_event_competition" }
{ "name" : "olympics.olympic_event_competition.$_id_" }
{ "name" : "olympics.olympic_games" }
has more
> it
{ "name" : "olympics.olympic_games.$_id_" }
{ "name" : "olympics.olympic_host_city" }
{ "name" : "olympics.olympic_host_city.$_id_" }
{ "name" : "olympics.olympic_mascot" }
{ "name" : "olympics.olympic_mascot.$_id_" }
{ "name" : "olympics.olympic_medal" }
{ "name" : "olympics.olympic_medal.$_id_" }
{ "name" : "olympics.olympic_medal_demonstration" }
{ "name" : "olympics.olympic_medal_demonstration.$_id_" }
{ "name" : "olympics.olympic_medal_honor" }
{ "name" : "olympics.olympic_medal_honor.$_id_" }
{ "name" : "olympics.olympic_participating_country" }
{ "name" : "olympics.olympic_participating_country.$_id_" }
{ "name" : "olympics.olympic_sport" }
{ "name" : "olympics.olympic_sport.$_id_" }
{ "name" : "olympics.olympic_venue" }
{ "name" : "olympics.olympic_venue.$_id_" }

The problem is I was using the namespace object with db.find(), not the collection object. I am already in the database scope with the use command.

Knowing this I get what I expected with the correct collection name.

> db.olympic_event.find();
{ "_id" : ObjectId("4c0fb666a5cd86585be7c0fd"), "name" : "Men's Boxing, Super Heavyweight +91kg", "id" : "/guid/9202a8c04000641f8000000008d88df9", "sport" : "Boxing", "demonstration_competitions" : "", "olympic_games_contested" : "2008 Summer Olympics,1984 Summer Olympics,2000 Summer Olympics,2004 Summer Olympics,1988 Summer Olympics,1996 Summer Olympics,1992 Summer Olympics", "competitions" : "Boxing at the 1984 Summer Olympics - Super Heavyweight ,Boxing at the 2000 Summer Olympics - Super Heavyweight,Boxing at the 1988 Summer Olympics - Super Heavyweight ,Boxing at the 2004 Summer Olympics - Super Heavyweight,Boxing at the 1992 Summer Olympics - Super Heavyweight ,Boxing at the 2008 Summer Olympics - Super heavyweight,Boxing at the 1996 Summer Olympics - Super Heavyweight" }
{ "_id" : ObjectId("4c0fb666a5cd86585be7c0fe"), "name" : "Men's Judo, 60 - 66kg (half-lightweight)", "id" : "/guid/9202a8c04000641f8000000008d88d0e", "sport" : "Judo", "demonstration_competitions" : "", "olympic_games_contested" : "2004 Summer Olympics,2000 Summer Olympics,2008 Summer Olympics", "competitions" : "Judo at the 2008 Summer Olympics – Men's Half Lightweight (66 kg),Judo at the 2000 Summer Olympics - Men's Half Lightweight (66 kg),Judo at the 2004 Summer Olympics - Men's Half Lightweight (66 kg)" }
{ "_id" : ObjectId("4c0fb666a5cd86585be7c0ff"), "name" : "Men's Tennis, Indoor Singles", "id" : "/guid/9202a8c04000641f8000000010be70e8", "sport" : "Tennis", "demonstration_competitions" : "", "olympic_games_contested" : "1912 Summer Olympics,1908 Summer Olympics", "competitions" : "Tennis at the 1908 Summer Olympics - Men's Indoor Singles,Tennis at the 1912 Summer Olympics - Men's Indoor Singles" }
...

It’s interesting that a collection name can contain a fullstop ‘.’ which is the delimiter in the command syntax. In my earlier observation I was not getting an error, only an empty response. For example you can do this.

> use test;
switched to db test
> db.foo.x.save({a: 1});
> db.foo.x.find();
{ "_id" : ObjectId("4c0fc1784ff83a6831364d57"), "a" : 1 }

MongoDB Experience: What's running in the DB

You can very easily find out the running threads in the database (e.g. like a MySQL SHOW PROCESSLIST) with db.currentOp.

> db.currentOp();
{ "inprog" : [ ] }

No much happening, however under some load you can see

> db.currentOp();
{
	"inprog" : [
		{
			"opid" : 27980,
			"active" : true,
			"lockType" : "write",
			"waitingForLock" : false,
			"secs_running" : 0,
			"op" : "insert",
			"ns" : "olympics.olympic_athlete",
			"client" : "127.0.0.1:63652",
			"desc" : "conn"
		}
	]
}
> db.currentOp();
{
	"inprog" : [
		{
			"opid" : 57465,
			"active" : true,
			"lockType" : "write",
			"waitingForLock" : false,
			"secs_running" : 0,
			"op" : "insert",
			"ns" : "olympics.olympic_athlete_affiliation",
			"client" : "127.0.0.1:63653",
			"desc" : "conn"
		}
	]
}

I was able to see these when I was Bulk Loading Data

The HTTPConsole at http://localhost:28017/ (for default installation) also shows you all client connections as well as more information per thread, database uptime, replication status and a DBTOP for recent namespaces. For example:

mongodb mactazosx.local:27017

db version v1.4.3, pdfile version 4.5
git hash: 47ffbdfd53f46edeb6ff54bbb734783db7abc8ca
sys info: Darwin broadway.local 9.8.0 Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 i386 BOOST_LIB_VERSION=1_40

dbwritelocked:  0 (initial)
uptime:    2851 seconds

assertions:

replInfo:

Clients:
Thread	OpId	Active	LockType	Waiting	SecsRunning	Op	NameSpace	Query	client	msg	progress
initandlisten	0		1			2004	test	{ name: /^local.temp./ }	0.0.0.0:0
snapshotthread	0		0			0			0.0.0.0:0
websvr	18		-1			2004	test._defaultCollection	{}	0.0.0.0:0
conn	83741		-1			2004	olympics.olympic_host_city	{}	127.0.0.1:63268
conn	83739		0			2004	?	{ getlasterror: 1.0 }	127.0.0.1:63756

time to get dblock: 0ms
# databases: 3
Cursors byLoc.size(): 0

replication
master: 0
slave:  0
initialSyncCompleted: 1

DBTOP  (occurences|percent of elapsed)
NS	total	Reads	Writes	Queries	GetMores	Inserts	Updates	Removes
GLOBAL	1	0.00%	1	0.00%	0	0.00%	1	0.00%	0	0.00%	0	0.00%	0	0.00%	0	0.00%
olympics.olympic_host_city	1	0.00%	1	0.00%	0	0.00%	1	0.00%	0	0.00%	0	0.00%	0	0.00%	0	0.00%

It was interesting to see a whatsmyuri command. Will need to investigate that further.

MongoDB Experience: Bulk Loading Data

mongoDB has a mongoimport command. The docs only shows the usage but not any examples. here are my first examples.

data1.csv

1
2
3
4
5
6
7
8
9
0

You need to specify your database (-d) and collection (-c) for importing. In my example, I also specified the collection fields with (-f)

The –file is actually optional, specifying the filename as the large argument also works.

mongoimport -d test -c foo -f a -type csv data
connected to: 127.0.0.1
imported 10 objects

NOTE: The default type is JSON, so you can get some nasty errors if you forget the csv type.

Wed Jun  9 11:18:26 Assertion: 10340:Failure parsing JSON string near: 1
0x68262 0x23968 0x250563 0x251c7b 0x24cb00 0x250280 0x1af6
 0   mongoimport                         0x00068262 _ZN5mongo11msgassertedEiPKc + 514
 1   mongoimport                         0x00023968 _ZN5mongo8fromjsonEPKc + 520
 2   mongoimport                         0x00250563 _ZN6Import9parseLineEPc + 131
 3   mongoimport                         0x00251c7b _ZN6Import3runEv + 2635
 4   mongoimport                         0x0024cb00 _ZN5mongo4Tool4mainEiPPc + 2880
 5   mongoimport                         0x00250280 main + 496
 6   mongoimport                         0x00001af6 start + 54
exception:Failure parsing JSON string near: 1

In my second example I’m adding multiple fields. This time my data file also has a headers which you can ignore with (–headerline)

data2.csv

name, age
Mickey Mouse,65
Minnie Mouse,64
Donald Duck,
Taz Devil,22
Marvin the Martian,45
$ mongoimport -d test -c foo -f name,age -type csv --headerline data2.csv
connected to: 127.0.0.1
imported 6 objects
> db.foo.find();
...
{ "_id" : ObjectId("4c0fb0dfa5cd86585be6ca63"), "a" : 0 }
{ "_id" : ObjectId("4c0fb2bea5cd86585be6ca64"), "name" : "Mickey Mouse", "age" : 65 }
{ "_id" : ObjectId("4c0fb2bea5cd86585be6ca65"), "name" : "Minnie Mouse", "age" : 64 }
{ "_id" : ObjectId("4c0fb2bea5cd86585be6ca66"), "name" : "Donald Duck" }
{ "_id" : ObjectId("4c0fb2bea5cd86585be6ca67"), "name" : "Taz Devil", "age" : 22 }
{ "_id" : ObjectId("4c0fb2bea5cd86585be6ca68"), "name" : "Marvin the Martian", "age" : 45 }

You can also use the –drop argument to truncate your collection before loading.

Real Data

I’m going to use the Freebase Olympics data to perform a more robust test.

wget http://download.freebase.com/datadumps/2010-04-15/browse/olympics.tar.bz2
bunzip2 olympics.tar.bz2
tar xvf olympics.tar
cd olympics

Loading this data via the following convenience script gave me some more meaningful data.

> db.olympic_host_city.find();
{ "_id" : ObjectId("4c0fb666a5cd86585be7d9b6"), "name" : "Vancouver", "id" : "/guid/9202a8c04000641f80000000000401e2", "olympics_hosted" : "2010 Winter Olympics" }
{ "_id" : ObjectId("4c0fb666a5cd86585be7d9b7"), "name" : "Moscow", "id" : "/guid/9202a8c04000641f800000000002636c", "olympics_hosted" : "1980 Summer Olympics" }
{ "_id" : ObjectId("4c0fb666a5cd86585be7d9b8"), "name" : "St. Moritz", "id" : "/guid/9202a8c04000641f80000000001c33e8", "olympics_hosted" : "1948 Winter Olympics,1928 Winter Olympics" }
...

Here is the simple load script I used.

#!/bin/sh

load_file() {
  local INPUT_FILE=$1
  [ -z "${INPUT_FILE}" ] && echo "ERROR: File not specified" && return 1

  echo "Loading file ${INPUT_FILE}"

  COLLECTION=`echo ${INPUT_FILE} | cut -d. -f1`

  FIELDS=`head -1 ${INPUT_FILE} | sed -e "s/	/,/g;s/ /_/g"`
  echo "mongoimport -d olympics -c ${COLLECTION} -type tsv --headerline -f $FIELDS --drop ${INPUT_FILE}"
  time mongoimport -d olympics -c ${COLLECTION} -type tsv --headerline -f $FIELDS --drop ${INPUT_FILE}
  return 0
}

process_dir() {

  echo "Processing" `pwd`
  for FILE in `ls *.tsv`
  do
    load_file ${FILE}
  done

  return 0
}

main() {
  process_dir
}

main $*
exit 0

MongoDB Experience: Online Resources

Following the initial Quickstart docs you will find a lot of online documentation. The following are good places to start.

There is also a Getting Started however I found this a duplication of the Quickstart. I have not found an offline version of the manual, or a single HTML page version. This makes it a little difficult for reading without internet connectivity.

You can find information at the Official Blog. While I found no Blog Roll, one developer Kyle Banker has a blog.

There are several Mailing Lists available however It seems your best help may be via IRC at irc://irc.freenode.net/#mongodb I found over 200 members on the channel.

There are currently no books on MongoDB however there seems to be 4 books in the making.

MongoDB Experience: Getting Started

Getting started with MongoDB is relatively straight forward, following the instructions from the Quickstart guide has you operational in a few minutes.

I like projects that provide a latest version link for software. There is no need to update any documentation or blog posts over time. The current instructions require some additional steps when creating the initial data directory, due to normal permissions of the root directory. This is the only pre-requisite to using the software out of the box. There is no additional configuration required for a default installation.

$ sudo mkdir /data/db
$ sudo chown `id -u` /data/db

I ran a few boundary tests to verify the error handling of the initial startup process.

The following occurs when the data directory does not exist.

$ ./mongodb-osx-i386-1.4.3/bin/mongod
./mongodb-osx-i386-1.4.3/bin/mongod --help for help and startup options
Tue Jun  8 15:59:52 Mongo DB : starting : pid = 78161 port = 27017 dbpath = /data/db/ master = 0 slave = 0  32-bit

** NOTE: when using MongoDB 32 bit, you are limited to about 2 gigabytes of data
**       see http://blog.mongodb.org/post/137788967/32-bit-limitations for more

Tue Jun  8 15:59:52 Assertion: 10296:dbpath (/data/db/) does not exist
0x68572 0x247814 0x24821a 0x24a855 0x1e06
 0   mongod                              0x00068572 _ZN5mongo11msgassertedEiPKc + 514
 1   mongod                              0x00247814 _ZN5mongo14_initAndListenEiPKc + 548
 2   mongod                              0x0024821a _ZN5mongo13initAndListenEiPKc + 42
 3   mongod                              0x0024a855 main + 4917
 4   mongod                              0x00001e06 start + 54
Tue Jun  8 15:59:52   exception in initAndListen std::exception: dbpath (/data/db/) does not exist, terminating
Tue Jun  8 15:59:52  dbexit:
Tue Jun  8 15:59:52 	 shutdown: going to close listening sockets...
Tue Jun  8 15:59:52 	 shutdown: going to flush oplog...
Tue Jun  8 15:59:52 	 shutdown: going to close sockets...
Tue Jun  8 15:59:52 	 shutdown: waiting for fs preallocator...
Tue Jun  8 15:59:52 	 shutdown: closing all files...
Tue Jun  8 15:59:52      closeAllFiles() finished
Tue Jun  8 15:59:52  dbexit: really exiting now

The following error occurs when the user has insufficient permissions for the directory.

$ sudo mkdir /data/db
$ ./mongodb-osx-i386-1.4.3/bin/mongod
./mongodb-osx-i386-1.4.3/bin/mongod --help for help and startup options
Tue Jun  8 16:01:52 Mongo DB : starting : pid = 78178 port = 27017 dbpath = /data/db/ master = 0 slave = 0  32-bit

** NOTE: when using MongoDB 32 bit, you are limited to about 2 gigabytes of data
**       see http://blog.mongodb.org/post/137788967/32-bit-limitations for more

Tue Jun  8 16:01:52 User Exception 10309:Unable to create / open lock file for dbpath: /data/db/mongod.lock
Tue Jun  8 16:01:52   exception in initAndListen std::exception: Unable to create / open lock file for dbpath: /data/db/mongod.lock, terminating
Tue Jun  8 16:01:52  dbexit:
Tue Jun  8 16:01:52 	 shutdown: going to close listening sockets...
Tue Jun  8 16:01:52 	 shutdown: going to flush oplog...
Tue Jun  8 16:01:52 	 shutdown: going to close sockets...
Tue Jun  8 16:01:52 	 shutdown: waiting for fs preallocator...
Tue Jun  8 16:01:52 	 shutdown: closing all files...
Tue Jun  8 16:01:52      closeAllFiles() finished
Tue Jun  8 16:01:52 	 shutdown: removing fs lock...
Tue Jun  8 16:01:52 	 couldn't remove fs lock errno:9 Bad file descriptor
Tue Jun  8 16:01:52  dbexit: really exiting now

A missing step from the existing documentation is to set appropriate permissions to the data directory so that mongod run as your normal user can write to the directory.

$ sudo chown `id -u` /data/db
$ ./mongodb-osx-i386-1.4.3/bin/mongod

Tue Jun  8 16:06:37 Mongo DB : starting : pid = 78284 port = 27017 dbpath = /data/db/ master = 0 slave = 0  32-bit

** NOTE: when using MongoDB 32 bit, you are limited to about 2 gigabytes of data
**       see http://blog.mongodb.org/post/137788967/32-bit-limitations for more

Tue Jun  8 16:06:37 db version v1.4.3, pdfile version 4.5
Tue Jun  8 16:06:37 git version: 47ffbdfd53f46edeb6ff54bbb734783db7abc8ca
Tue Jun  8 16:06:37 sys info: Darwin broadway.local 9.8.0 Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 i386 BOOST_LIB_VERSION=1_40
Tue Jun  8 16:06:37 waiting for connections on port 27017
Tue Jun  8 16:06:37 web admin interface listening on port 28017

You are then ready to rock and roll. Use the exit command to exit the mongo interactive shell.

$ ./mongodb-osx-i386-1.4.3/bin/mongo
> db.foo.save ({a:2});
> db.foo.find();
{ "_id" : ObjectId("4c0ea308f5ea2f7148a33b9f"), "a" : 2 }
> exit
bye

The mongod output of the first save of data into the “foo” collection shows a little of how mongodb operations. There is a lazy instantiation of “test” database when first required. There is no need to first create this, or use this as with MySQL.

Tue Jun  8 16:07:36 allocating new datafile /data/db/test.ns, filling with zeroes...
Tue Jun  8 16:07:36 done allocating datafile /data/db/test.ns, size: 16MB, took 0.05 secs
Tue Jun  8 16:07:37 allocating new datafile /data/db/test.0, filling with zeroes...
Tue Jun  8 16:07:38 done allocating datafile /data/db/test.0, size: 64MB, took 1.282 secs
Tue Jun  8 16:07:40 building new index on { _id: 1 } for test.foo
Tue Jun  8 16:07:40 Buildindex test.foo idxNo:0 { name: "_id_", ns: "test.foo", key: { _id: 1 } }
Tue Jun  8 16:07:40 done for 0 records 0.018secs
Tue Jun  8 16:07:40 insert test.foo 3181ms
$ ls -l /data/db
total 163848
drwxr-xr-x  2 rbradfor  admin        68 Jun  8 16:07 _tmp
-rwxr-xr-x  1 rbradfor  admin         6 Jun  8 16:06 mongod.lock
-rw-------  1 rbradfor  admin  67108864 Jun  8 16:07 test.0
-rw-------  1 rbradfor  admin  16777216 Jun  8 16:07 test.ns

One observation is the output of the mongod is more a trace output. I have yet to see any information about a more appropriately formatted error log.

MongoDB Experience: History

My first exposure to MongoDB was in July 2008 when I was a panelist on “A Panel on Cloud Computing” at the Entrepreneurs Round Table in New York. The panel included a representative from 10gen the company behind the open source database product and at the time Mongo was described as a full stack solution with the database being only one future component.

While I mentioned Mongo again in a blog in Nov 2008, it was not until Oct 6 2009 at the NoSQL event in New York where I saw a more stable product and a revised focus of development just on the database component.

As the moderator for the closing keynote “SQL v NOSQL” panel at Open SQL Camp 2009 in Portland, Oregon I had the chance to discuss MongoDB with the other products in the NoSQL space. Watch Video

In just the past few weeks, 3 people independently have mentioned MongoDB and asked for my input. I was disappointed to just miss the MongoNYC 2010 event.

While I have evaluated various new products in the key/value store and the schemaless space, my curiosity has been initially more with Cassandra and CouchDB.

Follow my journey as I explore in more detail the usage of mongoDB {name: “mongo”, type:”db”} via the mongodb tag on my blog.

Oracle resources for the MySQL Community

While I have spent a lot of time recently helping the MySQL community interact with and integrate with various Oracle User Groups including ODTUG, IOUG, NoCOUG, NYOUG, DAOG I thought I’d share some resources for the MySQL Community that wanted to know more about Oracle.

The Oracle family of products is huge. You only have to look at the acquisitions via Wikipedia to get an idea. The first thing is to narrow your search, e.g. Database, APEX, Middleware, BI, Hyperion, Financials, development via Java, PHP or Oracle Forms etc.

While Oracle is a commercial product you can download all software for FREE via Oracle Technology Network. There is also documentation, forums, blogs and events.

Some Oracle bloggers I have already been reading however I’m expanding my list. People you may want to consider include:

Cary Millsap,Lewis Cunningham, Debra Lilley, Dimitri Gielis,Duncan Mills, Edward Roske, Mark Rittman, Scott Spendolini, Tim Tow, Tom Kyte

If you want a comparison of the Oracle and MySQL community, be sure to also check out Sheeri Cabral’s keynote address at the 2010 MySQL User Conference for reference.

I'll have a MySQL shot to go!

Wednesday night of the MySQL track of ODTUG Kaleidoscope will include an evening with Last Comic Standing comedian, John Heffron. It should be great way to unwind after day 3 of the conference. Black vodka anybody.

Check out the MySQL Schedule for more information of presentations for the 4 days. More details is also available here.

When SET GLOBAL affects SESSION scope

We have all been caught out with using SET and not realizing that the default GLOBAL Scope (since 5.0.2) does not change the current SESSION scope.

I was not aware until today that changing GLOBAL scope has some exceptions that also automatically affect SESSION scope.

What I expected with a change in the GLOBAL scope is no affect SESSION scope. For example.

mysql> SHOW GLOBAL VARIABLES LIKE 'read_buffer_size';
+------------------+--------+
| Variable_name    | Value  |
+------------------+--------+
| read_buffer_size | 131072 |
+------------------+--------+
1 row in set (0.00 sec)

mysql> SHOW SESSION VARIABLES LIKE 'read_buffer_size';
+------------------+--------+
| Variable_name    | Value  |
+------------------+--------+
| read_buffer_size | 131072 |
+------------------+--------+
1 row in set (0.00 sec)

mysql> SET GLOBAL read_buffer_size=1024*256;
Query OK, 0 rows affected (0.00 sec)

mysql> SHOW GLOBAL VARIABLES LIKE 'read_buffer_size';
+------------------+--------+
| Variable_name    | Value  |
+------------------+--------+
| read_buffer_size | 262144 |
+------------------+--------+
1 row in set (0.00 sec)

mysql> SHOW SESSION VARIABLES LIKE 'read_buffer_size';
+------------------+--------+
| Variable_name    | Value  |
+------------------+--------+
| read_buffer_size | 131072 |
+------------------+--------+
1 row in set (0.00 sec)

However I was no prepared for this when changing an important variable for transaction management.

mysql> SHOW GLOBAL VARIABLES LIKE 'autocommit';
+---------------+-------+
| Variable_name | Value |
+---------------+-------+
| autocommit    | ON    |
+---------------+-------+
1 row in set (0.00 sec)

mysql> SHOW SESSION VARIABLES LIKE 'autocommit';
+---------------+-------+
| Variable_name | Value |
+---------------+-------+
| autocommit    | ON    |
+---------------+-------+
1 row in set (0.00 sec)

mysql> SET autocommit=0;
Query OK, 0 rows affected (0.00 sec)

mysql> SHOW GLOBAL VARIABLES LIKE 'autocommit';
+---------------+-------+
| Variable_name | Value |
+---------------+-------+
| autocommit    | OFF   |
+---------------+-------+
1 row in set (0.00 sec)

mysql> SHOW SESSION VARIABLES LIKE 'autocommit';
+---------------+-------+
| Variable_name | Value |
+---------------+-------+
| autocommit    | OFF   |
+---------------+-------+
1 row in set (0.00 sec)

However even more perplexing was the following message:

mysql> SET GLOBAL autocommit=0;
ERROR 1228 (HY000): Variable 'autocommit' is a SESSION variable and can't be used with SET GLOBAL

So this is another case were the definition of variables is not applicable in a GLOBAL level, yet the tools of the trade represent in some manner misleading information.
To prove my point, here is another new concurrent session started after the above.

mysql> SHOW GLOBAL VARIABLES LIKE 'autocommit';
+---------------+-------+
| Variable_name | Value |
+---------------+-------+
| autocommit    | ON    |
+---------------+-------+
1 row in set (0.01 sec)

mysql> SHOW SESSION VARIABLES LIKE 'autocommit';
+---------------+-------+
| Variable_name | Value |
+---------------+-------+
| autocommit    | ON    |
+---------------+-------+
1 row in set (0.00 sec)

The MySQL Documentation also had an incorrect specification with description regarding this scope, Bug #54215

Best Practices: Additional User Security

By default MySQL allows you to create user accounts and privileges with no password. In my earlier MySQL Best Practices: User Security I describe how to address the default installation empty passwords.

For new user accounts, you can improve this default behavior using the SQL_MODE variable, with a value of NO_AUTO_CREATE_USER. As detailed via the 5.1 Reference Manual

NO_AUTO_CREATE_USER

Prevent the GRANT statement from automatically creating new users if it would otherwise do so, unless a nonempty password also is specified.

Having set this variable I attempted to show the error of operation to demonstrate in my upcoming “MySQL Idiosyncrasies that bite” presentation.

Confirm Settings

mysql> show global variables like 'sql_mode';
+---------------+---------------------+
| Variable_name | Value               |
+---------------+---------------------+
| sql_mode      | NO_AUTO_CREATE_USER |
+---------------+---------------------+
1 row in set (0.00 sec)

mysql> show session variables like 'sql_mode';
+---------------+---------------------+
| Variable_name | Value               |
+---------------+---------------------+
| sql_mode      | NO_AUTO_CREATE_USER |
+---------------+---------------------+
1 row in set (0.00 sec)

Create error condition

mysql> CREATE USER [email protected];
Query OK, 0 rows affected (0.00 sec)
mysql> GRANT ALL ON *.* TO [email protected];
Query OK, 0 rows affected (0.00 sec)
mysql> exit

What the? Surely this isn’t right.

$ mysql -usuperuser

mysql> SHOW GRANTS;
+--------------------------------------------------------+
| Grants for [email protected]                         |
+--------------------------------------------------------+
| GRANT ALL PRIVILEGES ON *.* TO 'superuser'@'localhost' |
+--------------------------------------------------------+

mysql> SELECT VERSION();
+-----------+
| VERSION() |
+-----------+
| 5.1.39    |
+-----------+

Well that’s broken functionality.

What should happen as described in Bug #43938 is a cryptic message as reproduced below.

mysql> GRANT SELECT ON foo.* TO 'geert12'@'localhost';
ERROR 1133 (42000): Can't find any matching row in the user table
mysql> GRANT SELECT ON *.* TO [email protected] IDENTIFIED BY 'foobar';
Query OK, 0 rows affected (0.00 sec)

It seems however that the user of CREATE USER first nullifies this expected behavior, hence new Bug #54208.

Eventually consistent Group Commit

Having just written an interview response about NoSQL concepts for a RDBMS audience it was poetic that an inconspicuous title “(4 of 3)” highlights that both a MySQL read scalable implementation via replication and a NoSQL solution can share a common lack of timely consistency of data. For the sake of Group Commit I hope my data is always consistent at some location at some point in time as soon as possible.

In attempting to comment to Kristian Nielsen’s Fixing MySQL group commit (part 4 of 3) I was forced to watch an ad before I could even add a comment. Go jump Live Journal, it’s quicker to write my own blog post.

And if anybody is still reading, I had just written the following.

“There is clearly a place for NoSQL solutions. The two primary types of products are a key/value store and a schema-less solution. You need to learn the strengths, benefits and weaknesses of both. For a RDBMS resource the lack of transactions, the lack of joins and the concept of eventually consistent can take some time to accept.”

mk-query-digest Tips – Showing all hosts & users

The Maatkit tools provide a suite of additional MySQL commands. There is one command I use constantly and that is mk-query-digest.

Unfortunately the documentation does leave a lot to be desired for usability. While throughout, it is a man page and not a user guide. Several of us have discussed writing better documentation however it’s always a matter of time. I have however learned a number of tips and I’d like to share them in smaller digests.

The first is showing additional display. Maatkit works on truncating per line output to a reasonable length of 73 characters?

One of those lines is the list of hosts that connected to MySQL for a query, for example.

# Hosts                  4 192.168.40... (2), 192.168.40... (2)... 2 more
# Hosts                  3 99.99.245.14 (12), 999.106.206.167 (6)... 1 more

The problem is I want to know what that 1 more is so I can gather a complete list of IP addresses that connect to this server. You do that with the –show-all=host argument.

Without

$ cat external.tcpdump | ./mk-query-digest --type tcpdump | grep Hosts | uniq -c
#
      1 # Hosts                  3 99.99.245.14 (12), 999.106.206.167 (6)... 1 more
      1 # Hosts                  1 99.99.139.140

With

$ cat external.tcpdump | ./mk-query-digest --type tcpdump --show-all=host | grep Hosts | uniq -c
      1 # Hosts                  3 99.99.245.14 (12), 999.106.206.167 (6), 99.99.139.140 (2)
      1 # Hosts                  1 99.99.139.140

You can apply the same principle to the Users as well with –show-all=user

$ cat external.tcpdump | ./mk-query-digest --type tcpdump  --show-all=user | grep Users | uniq -c
      1 # Users                  2 xxx (13), phpmysqlmo... (5)
     49 # Users                  1  xxx

The problem is a still gett a truncation of the name ‘phpmysqlmo…’ That’s the one thing I’m trying to uncover, because that IP and usernme are not valid permissions for this system.