OMERO.server and PostgreSQL¶
In order to be installed, OMERO.server requires a running PostgreSQL instance that is configured to accept connections over TCP. This section explains how to ensure that you have the correct PostgreSQL version and that it is installed and configured correctly.
Ensuring you have a valid PostgreSQL version¶
For OMERO 5.6, PostgreSQL version 11 or later is recommended. Make sure you are using a supported version.
You can check which version of PostgreSQL you have installed with any of the following commands:
$ createuser -V createuser (PostgreSQL) 9.4.1 $ psql -V psql (PostgreSQL) 9.4.1 $ createdb -V createdb (PostgreSQL) 9.4.1
If your existing PostgreSQL installation is an earlier version, it is recommended that you upgrade to a more up-to-date version. Before upgrading, stop the OMERO server and then perform a full dump of the database using pg_dump. See the OMERO.server backup and restore section for further details.
If using a Linux distribution-provided PostgreSQL server, upgrading to a newer version of the distribution will usually make a newer version of PostgreSQL available. If the database was not migrated to the new version automatically, restore your backup after installing, configuring and starting the new version of the database server. If a PostgreSQL server was not provided by your system, EnterpriseDB provide an installer.
Checking PostgreSQL port listening status¶
You can check if PostgreSQL is listening on the default port
TCP/5432) by running the following command:
$ netstat -an | egrep '5432.*LISTEN' tcp 0 0 0.0.0.0:5432 0.0.0.0:* LISTEN tcp 0 0 :::5432 :::* LISTEN
The exact output of this command will vary. The important
thing to recognize is whether or not a process is listening on
If you cannot find a process listening on
TCP/5432 you will need to
postgresql.conf file and enable PostgreSQL’s TCP listening
mode. The exact location of the
postgresql.conf file varies between
It may be helpful to locate it using the package manager (
dpkg) or by utilizing the
find command. Usually, the
PostgreSQL data directory (which houses the
file, is located under
$ sudo find /etc -name 'postgresql.conf' $ sudo find /usr -name 'postgresql.conf' $ sudo find /var -name 'postgresql.conf' /var/lib/postgresql/data/postgresql.conf
The PostgreSQL data directory is usually only readable by the
postgres so you will likely have to be
root in order to
Once you have found the location of the
postgresql.conf file on
your particular installation, you will need to enable TCP listening.
The area of the configuration file you are concerned about should look similar
#listen_addresses = 'localhost' # what IP address(es) to listen on; # comma-separated list of addresses; # defaults to 'localhost', '*' = all #port = 5432 max_connections = 100 # note: increasing max_connections costs ~400 bytes of shared memory per # connection slot, plus lock space (see max_locks_per_transaction). You # might also need to raise shared_buffers to support more connections. #superuser_reserved_connections = 2 #unix_socket_directory = * #unix_socket_group = * #unix_socket_permissions = 0777 # octal #bonjour_name = * # defaults to the computer name
PostgreSQL HBA (host based authentication)¶
OMERO.server must have permission to connect to the database that has
been created in your PostgreSQL instance. This is configured in the
host based authentication file,
pg_hba.conf. Check the
configuration by examining the contents of
important that at least one line allows connections from the loopback
127.0.0.1) as follows:
# TYPE DATABASE USER CIDR-ADDRESS METHOD # IPv4 local connections: host all all 127.0.0.1/32 md5 # IPv6 local connections: host all all ::1/128 md5
The other lines that are in your
pg_hba.conf are important
either for PostgreSQL internal commands to work or for existing
applications you may have. Do not delete them.
After making any configuration changes to
pg_hba.conf, reload the server for the changes to take effect.
$ sudo service postgresql reload
Interactive documentation for the current release of PostgreSQL.
- Connections and Authentication
Section of the PostgreSQL documentation about configuring the server using postgresql.conf.
- Client Authentication
Chapter of the PostgreSQL documentation about configuring client authentication with pg_hba.conf.