Software section

Every single item on this page will eventually be an article, series of articles, or even a complete section. Please jump in and start off a topic

This sort of list may be deprecated now that I know how to create dynamic page lists, and also use category displays on a page. Still, this serves as a "pages wanted" list, and so it will be around until it is replaced by something better.

Software Foundations

Apache

See Apache

Installation

To get started, installing MySQL on RHEL is as simple as

yum install mysql-server

. However, you might get a message that your system is not registered to Red Hat Subscription Management (RHN in the old days), and thus the packages are not visible. To remedy this, you would of course use subscription-manager to register the host with Red Hat Subscription Management.

/usr/bin/mysqladmin -u root password 'new-password'
/usr/bin/mysqladmin -u root -h `hostname` password 'new-password'
# but it's easier and better to run
/usr/bin/mysql_secure_installation
# which will give you the option of removing the test database and removing the anonymous user created by default.  This is a must for production servers.

You can start the MySQL daemon with:

cd /usr ; /usr/bin/mysqld_safe &

You can test the MySQL daemon with mysql-test-run.pl

cd /usr/mysql-test ; perl mysql-test-run.pl

It's a good idea to setup a local configuration file for the system 'root' user, who can connect to the database server as db user 'root' by default when using the mysql command line client (ie. when you are user 'root' and type 'mysql' at the command line in a bash shell)

cat /root/.my.cnf

[client]
user=root
password=giveMeSomeDBgoodne55

Create a DB and user

CREATE DATABASE mediawiki;
GRANT ALL PRIVILEGES ON mediawiki.* TO 'example_user'@'localhost' IDENTIFIED BY 'secretpass';

Set Password for Root user

The following command issues a new password for the root user while at the same time dictating which authentication plugin to use.

ALTER USER 'root'@'localhost' IDENTIFIED WITH mysql_native_password BY 'secretpass';

Note: Since the introduction of Pluggable Authentication in MySQL 5.7 and also MariaDB since 5.2, there is a "unix_socket" plugin which authenticates the current user by their login to the OS, and thus NOT a password. If you have trouble setting the password, it's probably because you need to also specify the mysql_native_password auth at the same time

What's going on?

Want to find out what's going on in your MySQL server, but don't want to install client tools and access? Just make sure that the General Query Log is turned on, and tail the log file:

SHOW VARIABLES LIKE "general_log%";

+------------------+----------------------------+
| Variable_name    | Value                      |
+------------------+----------------------------+
| general_log      | OFF                        |
| general_log_file | /var/run/mysqld/mysqld.log |
+------------------+----------------------------+

mysql> SET GLOBAL general_log = 'ON';

Then you can tail the log file to see what it's doing:

tail -f /var/run/mysqld/mysqld.log

Be sure to turn off the log or your disk will fill up and you will not be happy.

mysql> SET GLOBAL general_log = 'OFF';

If you want more info than you can get from the direct query logging, then try [1]

Show grants

SHOW GRANTS only shows privs for the current user.

show grants;
show grants for 'root'@'localhost';

But this bash one-liner will show you all grants. -B --batch disables interactive behavior and doesn't use the history file -N --skip-column-names -e --execute executes a command and quits (disables --force and history file.)

mysql -B -N -e "SELECT DISTINCT CONCAT('SHOW GRANTS FOR ''',user,'''@''',host,''';') AS query FROM user" mysql | mysql

Fixing CHARSET and COLLATION

See the article about Collation

Working at the Console

Reading output from the mysql command line client is notoriously ugly/hard. With the -s --silent or -B --batch options, you can get output that is more readable.

Experts

Rick James https://mysql.rjweb.org/

Major Hayden https://major.io/tags/database/ https://github.com/major

Tools

Aside from mysqldump, there are also mysqlcheck, mysql_upgrade and other client programs.

1. MySQL Workbench is a great visual tool, but behind several obstacles and Oracles.
2. DBeaver
3. MySQLTuner by the aforementioned Major Hayden (he made a Python version too)
4. Percona Toolkit wget https://downloads.percona.com/downloads/percona-toolkit/3.5.7/binary/redhat/8/x86_64/percona-toolkit-3.5.7-1.el8.x86_64.rpm dnf install percona-toolkit-3.5.7-1.el8.x86_64.rpm pt-mysql-summary
5. http://mysqlsandbox.net/index.html MySQL sandbox could be useful for playing around with multiple databases in development.

Logs

Your data directory can fill up with binary logs unless you rotate them.

Information below comes from https://dba.stackexchange.com/questions/41050/is-it-safe-to-delete-mysql-bin-files

Don't just delete the files. Use MySQL to do it.

Either pass the name of a particular file, or a timestamp and MySQL will clear out the binary logs up to the one just specified (or the date)

Example 

-- consolidate the logs up to midnight 3 days ago
PURGE BINARY LOGS BEFORE DATE(NOW() - INTERVAL 3 DAY) + INTERVAL 0 SECOND;
-- consolidate the logs up to the file specified
PURGE BINARY LOGS TO `mysql-bin.000223`;

Which File to choose?

If you want to know which log files are in use so that you can remove superfluous ones without interrupting replication, go to your slave database and issue SHOW SLAVE STATUS\G

You'll see entries for

• Master_Log_File
• Relay_Master_Log_File

When replication has little or no lag these are usually the same value. If there is a lot of replication lag, they will be different values. Choose the value for Relay_Master_Log_File just to be safe. Go back to the DB master and issue PURGE BINARY LOGS TO mysql-bin.000337 where mysql-bin.000337 is the value of Relay_Master_Log_File

Persistence 

To persist this setup so your data directory doesn't fill up again, issue

SET GLOBAL expire_logs_days = 3;

To put the setting into effect immediately. And for the next time MySQL is restarted, add to /etc/my.cnf

[mysqld] 

expire_logs_days=3

Since the binlongs are used to recover the database state after a crash, this assumes that you are making database backups every day. If you only backup once per week, you would want at least 7 days worth of binlogs.

Tuning Reference

1. https://mariadb.com/kb/en/library/configuring-mariadb-for-optimal-performance
2. https://www.experts-exchange.com/questions/29060302/Tune-MySQL-to-32GB-RAM.html
3. https://www.tecmint.com/mysql-mariadb-performance-tuning-and-optimization/
4. https://www.percona.com/blog/10-mysql-performance-tuning-settings-after-installation/
5. https://www.percona.com/blog/2016/10/12/mysql-5-7-performance-tuning-immediately-after-installation/
6. https://www.percona.com/blog/2009/11/16/table_cache-negative-scalability/

MediaWiki

As of 2024-04-23 MediaWiki only requires MariaDB 10.3.x or MySQL 5.7.x for installation However, these are out of support. MariaDB is available in versions ranging from 10.4 - 10.11 and 11.0 - 11.5 The latest release in the 10.4 series is 10.4.33, released on 2024-02-07

Practically, this means that even if the database doesn't show errors, it could become vulnerable to attack or corruption at any time. And, tools like MySQLTuner, VSCode, PHPMyAdmin, etc. may not support the old version any longer.

Starting in REL1_35, MediaWiki uses the Doctrine Database Abstraction Layer (DBAL)

PHP

Getting PHP5 installed can be daunting. It still is not packaged for Debian stable. If you want a deb, add Dotdeb.org to your sources list. http://www.dotdeb.org/

Graphics

GIMP

GNU Image Manipulation Program The free software equivalent to Adobe PhotoShop.

Fotoxx

Fotoxx is a photo library management and editing tool Videos of using Fotoxx

Shotwell

Shotwell is my primary photo management and publishing tool (publishes to Google Photos and others).

Database

Installation

To get started, installing MySQL on RHEL is as simple as

yum install mysql-server

. However, you might get a message that your system is not registered to Red Hat Subscription Management (RHN in the old days), and thus the packages are not visible. To remedy this, you would of course use subscription-manager to register the host with Red Hat Subscription Management.

/usr/bin/mysqladmin -u root password 'new-password'
/usr/bin/mysqladmin -u root -h `hostname` password 'new-password'
# but it's easier and better to run
/usr/bin/mysql_secure_installation
# which will give you the option of removing the test database and removing the anonymous user created by default.  This is a must for production servers.

You can start the MySQL daemon with:

cd /usr ; /usr/bin/mysqld_safe &

You can test the MySQL daemon with mysql-test-run.pl

cd /usr/mysql-test ; perl mysql-test-run.pl

It's a good idea to setup a local configuration file for the system 'root' user, who can connect to the database server as db user 'root' by default when using the mysql command line client (ie. when you are user 'root' and type 'mysql' at the command line in a bash shell)

cat /root/.my.cnf

[client]
user=root
password=giveMeSomeDBgoodne55

Create a DB and user

CREATE DATABASE mediawiki;
GRANT ALL PRIVILEGES ON mediawiki.* TO 'example_user'@'localhost' IDENTIFIED BY 'secretpass';

Set Password for Root user

The following command issues a new password for the root user while at the same time dictating which authentication plugin to use.

ALTER USER 'root'@'localhost' IDENTIFIED WITH mysql_native_password BY 'secretpass';

Note: Since the introduction of Pluggable Authentication in MySQL 5.7 and also MariaDB since 5.2, there is a "unix_socket" plugin which authenticates the current user by their login to the OS, and thus NOT a password. If you have trouble setting the password, it's probably because you need to also specify the mysql_native_password auth at the same time

What's going on?

Want to find out what's going on in your MySQL server, but don't want to install client tools and access? Just make sure that the General Query Log is turned on, and tail the log file:

SHOW VARIABLES LIKE "general_log%";

+------------------+----------------------------+
| Variable_name    | Value                      |
+------------------+----------------------------+
| general_log      | OFF                        |
| general_log_file | /var/run/mysqld/mysqld.log |
+------------------+----------------------------+

mysql> SET GLOBAL general_log = 'ON';

Then you can tail the log file to see what it's doing:

tail -f /var/run/mysqld/mysqld.log

Be sure to turn off the log or your disk will fill up and you will not be happy.

mysql> SET GLOBAL general_log = 'OFF';

If you want more info than you can get from the direct query logging, then try [2]

Show grants

SHOW GRANTS only shows privs for the current user.

show grants;
show grants for 'root'@'localhost';

But this bash one-liner will show you all grants. -B --batch disables interactive behavior and doesn't use the history file -N --skip-column-names -e --execute executes a command and quits (disables --force and history file.)

mysql -B -N -e "SELECT DISTINCT CONCAT('SHOW GRANTS FOR ''',user,'''@''',host,''';') AS query FROM user" mysql | mysql

Fixing CHARSET and COLLATION

See the article about Collation

Working at the Console

Reading output from the mysql command line client is notoriously ugly/hard. With the -s --silent or -B --batch options, you can get output that is more readable.

Experts

Rick James https://mysql.rjweb.org/

Major Hayden https://major.io/tags/database/ https://github.com/major

Tools

Aside from mysqldump, there are also mysqlcheck, mysql_upgrade and other client programs.

1. MySQL Workbench is a great visual tool, but behind several obstacles and Oracles.
2. DBeaver
3. MySQLTuner by the aforementioned Major Hayden (he made a Python version too)
4. Percona Toolkit wget https://downloads.percona.com/downloads/percona-toolkit/3.5.7/binary/redhat/8/x86_64/percona-toolkit-3.5.7-1.el8.x86_64.rpm dnf install percona-toolkit-3.5.7-1.el8.x86_64.rpm pt-mysql-summary
5. http://mysqlsandbox.net/index.html MySQL sandbox could be useful for playing around with multiple databases in development.

Logs

Your data directory can fill up with binary logs unless you rotate them.

Information below comes from https://dba.stackexchange.com/questions/41050/is-it-safe-to-delete-mysql-bin-files

Don't just delete the files. Use MySQL to do it.

Either pass the name of a particular file, or a timestamp and MySQL will clear out the binary logs up to the one just specified (or the date)

Example 

-- consolidate the logs up to midnight 3 days ago
PURGE BINARY LOGS BEFORE DATE(NOW() - INTERVAL 3 DAY) + INTERVAL 0 SECOND;
-- consolidate the logs up to the file specified
PURGE BINARY LOGS TO `mysql-bin.000223`;

Which File to choose?

If you want to know which log files are in use so that you can remove superfluous ones without interrupting replication, go to your slave database and issue SHOW SLAVE STATUS\G

You'll see entries for

• Master_Log_File
• Relay_Master_Log_File

When replication has little or no lag these are usually the same value. If there is a lot of replication lag, they will be different values. Choose the value for Relay_Master_Log_File just to be safe. Go back to the DB master and issue PURGE BINARY LOGS TO mysql-bin.000337 where mysql-bin.000337 is the value of Relay_Master_Log_File

Persistence 

To persist this setup so your data directory doesn't fill up again, issue

SET GLOBAL expire_logs_days = 3;

To put the setting into effect immediately. And for the next time MySQL is restarted, add to /etc/my.cnf

[mysqld] 

expire_logs_days=3

Since the binlongs are used to recover the database state after a crash, this assumes that you are making database backups every day. If you only backup once per week, you would want at least 7 days worth of binlogs.

Tuning Reference

1. https://mariadb.com/kb/en/library/configuring-mariadb-for-optimal-performance
2. https://www.experts-exchange.com/questions/29060302/Tune-MySQL-to-32GB-RAM.html
3. https://www.tecmint.com/mysql-mariadb-performance-tuning-and-optimization/
4. https://www.percona.com/blog/10-mysql-performance-tuning-settings-after-installation/
5. https://www.percona.com/blog/2016/10/12/mysql-5-7-performance-tuning-immediately-after-installation/
6. https://www.percona.com/blog/2009/11/16/table_cache-negative-scalability/

MediaWiki

As of 2024-04-23 MediaWiki only requires MariaDB 10.3.x or MySQL 5.7.x for installation However, these are out of support. MariaDB is available in versions ranging from 10.4 - 10.11 and 11.0 - 11.5 The latest release in the 10.4 series is 10.4.33, released on 2024-02-07

Practically, this means that even if the database doesn't show errors, it could become vulnerable to attack or corruption at any time. And, tools like MySQLTuner, VSCode, PHPMyAdmin, etc. may not support the old version any longer.

Starting in REL1_35, MediaWiki uses the Doctrine Database Abstraction Layer (DBAL)

PHP is the HyperText Preprocessor = the most popular programming language for the web