Database Server Installation¶

Install MySQL¶

The following is for the computer that hosts the databases. This involves installing MySQL server and creation/configuration of the leginondb and projectdb databases.

1 Install MySQL-Server and MySQL-Client¶

Note: You may already have MySQL Server and Client installed. Check by typing mysql at the command line.
If you see a MySQL prompt (mysql>), you may skip this step.

To install Mysql on Linux you have two options (the first option is better):

1. Use your package installer (yum, zypper, YaST, apt-get). For example:
   

   sudo yum install mysql mysql-server

   
   For Suse
   

   yast2 -i mysql mysql-client

2. Download the latest MySQL-server package for Linux from http://www.mysql.com

2 Locate Example MySQL configuration files¶

They are usually located in /usr/share/mysql.

ls /usr/share/mysql/my*
    /usr/share/mysql/my-huge.cnf
    /usr/share/mysql/my-innodb-heavy-4G.cnf
    /usr/share/mysql/my-large.cnf
    /usr/share/mysql/my-medium.cnf
    /usr/share/mysql/my-small.cnf

If that does not work try the locate function

locate my | egrep "\.cnf$" 
    /etc/my.cnf
    /usr/share/mysql/my-huge.cnf
    /usr/share/mysql/my-innodb-heavy-4G.cnf
    /usr/share/mysql/my-large.cnf
    /usr/share/mysql/my-medium.cnf
    /usr/share/mysql/my-small.cnf

3 Configure my.cnf in /etc using my-huge.cnf as the template¶

1. Copy my-huge.cnf to my.cnf
   

   sudo cp -v /usr/share/mysql/my-huge.cnf /etc/my.cnf

2. Edit /etc/my.cnf to add or change query cache variables like these (be sure to place them under the [mysqld] section):
   

   query_cache_type = 1
   query_cache_size = 100M
   query_cache_limit= 100M
   

3. Search for the text default-storage-engine in /etc/my.cnf. If it exists and is set to other than MyISAM, you should change it to:
   

   default-storage-engine=MyISAM

4 Start the MySQL Server¶

For CentOS/Fedora/RHEL system use the service command:

sudo /sbin/service mysqld start

For other Unix systems:

sudo /etc/init.d/mysqld start

or on some installations (Suse),

sudo /etc/init.d/mysql start

For future reference: start | stop | restart MySQL Server with similar commands:

For Centos, Fedora

sudo /etc/init.d/mysqld start
sudo /etc/init.d/mysqld stop
sudo /etc/init.d/mysqld restart

or

sudo /sbin/service mysqld start
sudo /sbin/service mysqld stop
sudo /sbin/service mysqld restart

or for Suse

sudo /etc/init.d/mysql start
sudo /etc/init.d/mysql stop
sudo /etc/init.d/mysql restart

5 Configure MySQL to start automatically at boot¶

sudo /sbin/chkconfig mysqld on

or for SuSe:

sudo /sbin/chkconfig --add mysql

6 For future reference, the database location will be:¶

ls /var/lib/mysql
    ibdata1  ib_logfile0  ib_logfile1  mysql  mysql.sock  test

7 Create the Leginon database, call it leginondb¶

sudo mysqladmin create leginondb

8 Create the Project database, call it projectdb¶

sudo mysqladmin create projectdb

9 Connect to mysql db¶

If starting from scratch, the mysql root user will have no password. This is assumed to be the case and we will set it later.

mysql -u root mysql

You should see a mysql prompt: mysql>

You can view the current mysql users with the following command.

select user, password, host from user;
      +------+----------+-----------+
      | user | password | host      |
      +------+----------+-----------+
      | root |          | localhost |
      | root |          | host1     |
      |      |          | host1     |
      |      |          | localhost |
      +------+----------+-----------+
      4 rows in set (0.00 sec)

10 Create user¶

Create and grant privileges to a user called usr_object for the databases on both the localhost and other hosts involved. For example, use wild card '%' for all hosts. You can set specific (ALTER, CREATE, DROP, DELETE, INSERT, RENAME, SELECT, UPDATE) privileges or ALL privileges to the user. See MySQL Reference Manual for details. The following examples demonstrate some of the options available.

At the mysql prompt execute the following commands:

CREATE USER usr_object@'localhost' IDENTIFIED BY 'YOUR PASSWORD';
GRANT ALTER, CREATE, INSERT, SELECT, UPDATE ON leginondb.* TO usr_object@'localhost';
GRANT ALTER, CREATE, INSERT, SELECT, UPDATE ON projectdb.* TO usr_object@'localhost';

You may choose to use the following less secure version (no password and all privileges) of the commands above, however, we recommend not allowing the DROP and DELETE privileges.

At the mysql prompt execute the following commands:

CREATE USER usr_object@'localhost';
GRANT ALL PRIVILEGES ON leginondb.* TO usr_object@'localhost';
GRANT ALL PRIVILEGES ON projectdb.* TO usr_object@'localhost';

You may also choose to assign a domain to your commands and use a wildcard to allow access from all computers in the domain.

CREATE USER usr_object@'%.mydomain.edu' IDENTIFIED BY 'YOUR PASSWORD';
GRANT ALTER, CREATE, INSERT, SELECT, UPDATE ON leginondb.* to usr_object@'%.mydomain.edu';
GRANT ALTER, CREATE, INSERT, SELECT, UPDATE ON projectdb.* to usr_object@'%.mydomain.edu';

11 Give create and access privileges for the processing databases which begin with "ap".¶

# if your web host is local
GRANT ALTER, CREATE, INSERT, SELECT, UPDATE ON `ap%`.* to usr_object@localhost; 
# for all other hosts if you are accessing the databases from another computer
GRANT ALTER, CREATE, INSERT, SELECT, UPDATE ON `ap%`.* to usr_object@'%.mydomain.edu';       

12 Change Root password¶

To set the root password use the command:

sudo mysqladmin -u root password NEWPASSWORD

Or you can do it from within mysql

update user set password=password('your_own_root_password') where user="root";
Query OK, 2 rows affected (0.01 sec)
Rows matched: 2  Changed: 2  Warnings: 0

# run the flush privileges command to avoid problems
flush privileges;
^D or exit;

From now on, you will need to specify the password to connect to the database as root user like this:

mysql -u root -p mysql

13 Check MySQL variables¶

# at the command prompt, log into the leginon database

mysql -u usr_object -p leginondb

# At the mysql prompt show variables that begin with 'query'.
# Check that the changes you made to my.cfg are in place.

SHOW VARIABLES LIKE 'query%';
      +------------------------------+-----------+
      | Variable_name                | Value     |
      +------------------------------+-----------+
      | ft_query_expansion_limit     | 20        |
      | have_query_cache             | YES       |
      | long_query_time              | 10        |
      | query_alloc_block_size       | 8192      |
      | query_cache_limit            | 104857600 | ---This should correspond to your change
      | query_cache_min_res_unit     | 4096      |
      | query_cache_size             | 104857600 | ---This should correspond to your change
      | query_cache_type             | ON        | ---This should correspond to your change
      | query_cache_wlock_invalidate | OFF       |
      | query_prealloc_size          | 8192      |
      +------------------------------+-----------+
      10 rows in set (0.00 sec)

exit;

14 Make sure MySQL is running¶

mysqlshow -u root
      +--------------+
      | Databases    |
      +--------------+
      | mysql        |
      | leginondb    |
      | projectdb    |
      +--------------+

Run the following command from the command line:¶

php -r "mysql_connect('localhost', 'usr_object', 'PASSWORD', 'leginondb'); echo mysql_stat();"; echo "" 

Expected output:

Uptime: 1452562 Threads: 1 Questions: 618 Slow queries: 0 Opens: 117 Flush tables: 1 Open tables: 106 Queries per second avg: 0.000

If there are any error messages, mysql may be configured incorrectly.

Note: If you do not have php and php-mysql packages installed you need to install them to run the above command. The yum installation is:

sudo yum -y install php php-mysql

Configure phpMyAdmin¶

You are not required to install phpMyAdmin for Appion or Leginon, however, it is a useful tool for interfacing with the mysql databases.

Install prerequisites¶

Name:	Download site:	yum package name	SuSE rpm name
PHP	http://php.net/downloads.php	php
php-mysql		php-mysql

Install phpMyAdmin¶

If you have not already installed phpMyAdmin, do so. The yum installation is:

sudo yum -y install phpMyAdmin

Configure phpMyAdmin¶

Edit the phpMyAdmin config file /etc/phpMyAdmin/config.inc.php and change the following lines:

$cfg['Servers'][$i]['AllowRoot']     = FALSE;

Edit the phpMyAdmin apache config file /etc/httpd/conf.d/phpMyAdmin.conf and change the following lines:

<Directory /usr/share/phpMyAdmin/>
order deny,allow
deny from all
allow from 127.0.0.1
allow from YOUR_IP_ADDRESS
</Directory>

Note: If you want to access phpMyAdmin from another computer, you can also add it to this config file with an allow from tag

Restart Web Server¶

Next restart the web server to take on the new setting

sudo /sbin/service httpd restart

Test the configuration¶

To test the phpMyAdmin configuration, point your browser to http://YOUR_IP_ADDRESS/phpMyAdmin or http://localhost/phpMyAdmin and login with the usr_object user.

A common problem is that the firewall may be blocking access to the web server and mysql server. On CentOS/Fedora you can configure this with the system config:

system-config-securitylevel

Firewall configuration is specific to different Unix distributions, so consult a guide on how to do this on non-RedHat machines.