12.17. Linux flavours

12.17.1. Common administrative commands

Ubuntu

CentOS 6.5

System

Heritage

Debian

Red Hat Enterprise Linux

Package management

apt-get, dpkg, and for convenience gdebi

yum

General system update

sudo apt-get update && sudo apt-get dist-upgrade

sudo yum update

Package type

deb

rpm

Extra security

Nothing complex by default

SELinux; file permissions must be set with chcon

Autostarting daemons at boot

Usually happens automatically

Usually need to configure with chkconfig

Which OS version am I running?
lsb_release -a
uname -a
cat /etc/centos-release
uname -a

Python

Default Python versions (CamCOPS requires 3.4)

2.7, 3.4

2.6

Apache

Apache main configuration file

Usually /etc/apache2/apache2.conf

Usually /etc/httpd/conf/httpd.conf

Apache SSL configuration file

Usually /etc/apache2/sites-available/default-ssl

Usually /etc/httpd/conf.d/ssl.conf

Granting access in Apache config file
Apache 2.4:
Require all granted
Apache 2.2:
Order allow,deny
Allow from all

Default Apache system user

www-data

apache

Default SSL certificate location

/etc/ssl/

/etc/pki/tls/

Default Apache log directory

/var/log/apache2/

/var/log/httpd/

Restarting Apache

  • sudo service apache2 [start|stop|restart]

  • sudo apache2ctl [start|stop|restart]

  • sudo apachectl [start|stop|restart]

  • sudo service httpd [start|stop|restart]

  • sudo apachectl [start|stop|restart]

supervisord

supervisord configuration file

Usually /etc/supervisor/supervisord.conf

Usually /etc/supervisord.conf

Restarting supervisord

  • sudo service supervisor [start|stop|restart]

  • sudo supervisorctl

  • sudo service supervisord [start|stop|restart]

  • sudo supervisorctl

MySQL

Default MySQL configuration file

/etc/mysql/my.cnf

/etc/my.cnf

Restarting MySQL

sudo service mysql [start|stop|restart]

sudo service mysqld [start|stop|restart]

Default MySQL log

/var/log/mysql.log

/var/log/mysqld.log

CamCOPS packages

Installation

sudo gdebi install camcops_VERSION_all.deb

sudo yum install camcops_VERSION.noarch.rpm

Removal

sudo dpkg --remove camcops

sudo yum remove camcops

12.17.2. Installing CamCOPS prerequisites under RHEL 8.6

Probably also applicable to CentOS 8.x.

Ensure additional repositories are in use:

If accessing the internet through a proxy, where the https_proxy environment variable is defined, use: sudo -E to pass the environment to the superuser.

If /tmp has been securely mounted as noexec you will need to remount it as exec. Remove the noexec option from /etc/fstab and sudo mount -o remount /tmp. This will allow alien to execute scripts under /tmp. Otherwise you will get errors like /var/tmp/rpm-tmp.AbCDef: line 96: /tmp/alien.nnnnnnn/script: Permission denied when installing the package. You can remount /tmp``as ``noexec again after installation.

Potential prerequisites for what follows:

sudo dnf -y install python38 python38-devel python3-pip httpd mariadb-devel mod_ssl
sudo update-alternatives --config python3

12.17.3. Setting up MySQL under Linux

  1. Under Ubuntu, if you are happy to leave the data files at their default location, skip this step. Check/edit the MySQL configuration (see table above for filenames). See Getting Started with MySQL. In particular:

    • datadir should point to your database files (default often /var/lib/mysql, but /srv/mysql is one alternative).

    • Other options are explained here.

    • If you create a blank directory (such as /srv/mysql), you will need to use the mysql_install_db tool; see Postinstallation Setup and Testing; an example command is

      sudo mysql_install_db --user=mysql --basedir=/usr --datadir=/srv/mysql

    • Manual start: sudo /usr/bin/mysqld_safe –user=mysql &. Manual stop: sudo mysqladmin shutdown.

    • Service start/stop: see table above.

    • If it starts manually but not as a service (in a manner that depends on your data directory), you have a challenging problem; an option is to return to the default data directory!

    • To log in prior to securing the database: mysql.

    • See also the CentOS MySQL installation guide.

    • Default logfile: /var/log/mysqld.log or /var/log/mysql/…

  2. Secure your MySQL installation by running mysql_secure_installation.

    • Login after securing: mysql -u root -p.

    • Similar username/password requirements now apply to manual shutdowns.

  3. Ensure that the max_allowed_packet parameter is large enough.

    • This parameter needs to be set large enough that the largest binary large objects (BLOBs) can be uploaded. CamCOPS BLOBs are mostly photographs from tablets. A high-end tablet in 2014 might have an 8 megapixel (MP) camera, with each pixel taking 3 bytes, i.e. 24 Mb. Furthermore, the transfer takes more space thanks to somewhat inefficient encoding. The MySQL server default value is just 1 Mb 1.

    • You must set this parameter for the server, and for the mysqldump tool.

    • A suggested value is 32 Mb. Edit my.cnf to include max_allowed_packet values in the [mysqld] and [mysqldump] sections (creating them if necessary).

    • Similar editing of the [client] section of my.cnf is unnecessary, firstly because some other MySQL clients may not recognize the option and might choke on it, and secondly because CamCOPS uses MySQLdb (MySQL-Python), which uses the MySQL C API, which has a default limit of 1 Gb 2.

  4. Set some other MySQL parameters for TEXT-heavy tables; see Troubleshooting: Row size too large.

  5. Thus, edit my.cnf to include the following:

    [mysqld]
max_allowed_packet = 32M

innodb_strict_mode = 1
innodb_file_per_table = 1
innodb_file_format = Barracuda

# Only for MySQL prior to 5.7.5 (http://dev.mysql.com/doc/relnotes/mysql/5.6/en/news-5-6-20.html):
# innodb_log_file_size = 512M

[mysqldump]
max_allowed_packet = 32M

  6. Ensure MySQL is running as a service (as above).

  7. Create the CamCOPS database. See create a database.

Footnotes

1

http://dev.mysql.com/doc/refman/5.7/en/packet-too-large.html

2

http://dev.mysql.com/doc/refman/5.7/en/c-api.html