Note

This documentation is for OMERO 5.2. This version is now in maintenance mode and will only be updated in the event of critical bugs or security concerns. OMERO 5.3 is expected in the first quarter of 2017.

Grid configuration

In some cases, the configuration properties will not suffice to fully configure your server. In that case, it may be necessary to make use of IceGrid’s XML configuration files. Like the config.xml file mentioned above, these are stored under etc/grid: etc/grid/default.xml is used on Unix systems, etc/grid/windefault.xml is used on Windows systems and both make use of etc/grid/templates.xml.

The default OMERO application descriptor deploys multiple server instances (Blitz-0, FileServer, Indexer-0, PixelData-0, ...) on a single node. Each server instance is defined by a server-template element in etc/grid/templates.xml with its own parameters.

Modifying the application descriptors

When you run omero admin start without any other arguments, it looks up the default application descriptor for your platform:

$ bin/omero admin start
No descriptor given. Using etc/grid/default.xml
Waiting on startup. Use CTRL-C to exit

The “start” and “deploy” command, however, take several other parameters:

$ bin/omero admin start --help
usage: bin/omero admin start [-h] [-u USER] [file] [targets [targets ...]]

Start icegridnode daemon and waits for required components to come up,
i.e. status == 0

If the first argument can be found as a file, it will be deployed as the
application descriptor rather than etc/grid/default.xml. All other
arguments will be used as targets to enable optional sections of the
descriptor

Positional Arguments:
  file                  Application descriptor. If not provided, a default will be used
  targets               Targets within the application descriptor which should be activated.

If a file is passed in as the first argument, then that application descriptor as opposed to etc/grid/default.xml will be used. You can also modify the default application descriptors in place.

Note

The largest issue with using your own application descriptors or modifying the existing ones is that they tend to change between versions, and there is no facility for automatically merging your local changes. You should be prepared to re-make whatever changes you perform directly on the new files.

Targets

Targets are elements within the application descriptors which can optionally turn on configuration. The target is only applicable until the next invocation of omero admin start or omero admin deploy

Note

You must remember to always apply the targets on each omero admin command. If not, the target will not be removed. Therefore, they are often better used for debugging purposes; however, as opposed to alternative application descriptors, using the pre-existing targets should not require any special effort during upgrades.

Debugging

<properties id="PythonServer">
  <property name="Ice.ImplicitContext" value="Shared"/>
  <!-- Default logging settings for Python servers. -->
  <property name="omero.logging.timedlog" value="False"/>
  <property name="omero.logging.logsize" value="5000000"/>
  <property name="omero.logging.lognum" value="9"/>
  <property name="omero.logging.level" value="20"/>
  <target name="debug">
    <property name="omero.logging.level" value="10"/>
  </target>

Here, the “debug” target allows increasing the logging output of the Python servers without modifying any files.

JMX configuration

<server-template id="BlitzTemplate">
  <parameter name="index"/>
  <parameter name="config" default="default"/>
  <parameter name="jmxhost" default=""/>
  <parameter name="jmxport" default="3001"/>
   …
    <target name="jmx">
        <!-- Be sure to understand the consequences of enabling JMX.
             It allows calling remote methods on your JVM -->
        <option>-Dcom.sun.management.jmxremote=${jmxhost}</option>
        <option>-Dcom.sun.management.jmxremote.port=${jmxport}</option>
        <option>-Dcom.sun.management.jmxremote.authenticate=false</option>
        <option>-Dcom.sun.management.jmxremote.ssl=false</option>
    </target>

The JMX target activates the monitoring of the Blitz server via JMX. If you need to modify the “jmxport” or “jmxhost” variables, you will need to do so directly in the application descriptor XML.

Changing ports / multiple servers on a single host

By modifying the default OMERO ports, it is possible to run multiple OMERO servers on the same physical machine. All port numbers can be adjusted using the relevant configuration properties.

To run multiple servers on a single host, the easiest approach is to prefix all ports (SSL, TCP, registry) using omero.ports.prefix:

# First server
cd ~/OMERO.server-1
bin/omero admin start

# Second server
cd ~/OMERO.server-2
bin/omero config set omero.ports.prefix 1
bin/omero admin start

# Third server
cd ~/OMERO.server-3
bin/omero config set omero.ports.prefix 2
bin/omero admin start

Clients will need to use the appropriate port (4064, 14064 or 24064) to connect to OMERO.

See also

SSL

Section of the Server security and firewalls page.

Extending OMERO

Finally, if configuration does not suffice, there are also options for extending OMERO with your own code. These are described on the development site under Extending OMERO.server.