OMERO.grid

To unify the various components of OMERO, OMERO.grid was developed to monitor and control processes over numerous remote systems. Based on ZeroC’s IceGrid framework, OMERO.grid provides management access, distributed background processing, log handling and several other features.

Terminology

Please notice that ZeroC uses a specific naming scheme for IceGrid elements and actors. A server in the context of this document is not a host computer - it is a process running inside an IceGrid node, servicing incoming requests. A host is a computer on which IceGrid elements get deployed. For more details, see Terminology.

Getting started

Requirements

The normal OMERO installation actually makes use of OMERO.grid internally. If you have followed the instructions under OMERO.server installation you will have everything you need to start working with OMERO.grid.

The standard install should also be used to install other hosts in the grid, such as a computation-only host. Some elements can be omitted for a computation-only host such as PostgreSQL, Apache/nginx, etc.

Running OMERO.web and/or starting up the full OMERO.server instance is not required in such a case (only the basic requirements to run omero node are needed, i.e. ZeroC Ice and Python modules for OMERO scripts).

IceGrid Tools

If you would like to explore your IceGrid configuration, use

omero admin ice

It provides full access to the icegridadmin console described in the ZeroC manual. Specific commands can also be executed:

omero admin ice help
omero admin ice application list
omero admin ice application describe OMERO
omero admin ice server list

Further, by running java -jar ice-gridgui.jar the GUI provided by ZeroC can be used to administer OMERO.grid. This JAR is provided in the OMERO source code under lib/repository.

How it works

IceGrid is a location and activation service, which functions as a central registry to manage all your OMERO server processes. OMERO.grid provides server components which use the registry to communicate with one another. Other than a minimal amount of configuration and starting a single daemon on each host machine, OMERO.grid manages the complexity of all your computing resources.

Deployment descriptors

All the resources for a single OMERO site are described by one application descriptor. OMERO ships with several example descriptors under etc/grid. These descriptors describe what processes will be started on what nodes, identified by simple names. For example the default descriptor, used if no other file is specified, defines the master node. As you will see, these files are critical both for the correct functioning of your server as well as its security.

The deployment descriptors provided define which server instances are started on which nodes. The default descriptor configures the master node to start the OMERO.blitz server, the Glacier2 router for firewalling, as well as a single processor - Processor0. The master node is also configured via etc/master.cfg to host the registry, though this process can be started elsewhere.

Deployment commands

The master node must be started first to provide the registry. This is done via the omero admin start command which uses the default descriptor:

omero admin start

The deploy command looks for any changes to the defined descriptor and restarts only those servers which have modifications:

omero admin deploy

Both omero admin start and omero admin deploy can optionally take a path to an application descriptor which must be passed on every invocation:

omero admin deploy etc/grid/my-site.xml

Two other nodes, then, each provide a single processor, Processor1 and Processor2. These are started via:

To start a node identified by NAME, the following command can be used

omero node start NAME

At this point the node will try and connect to the registry to announce its presence. If a node with the same name is already started, then registration will fail, which is important to prevent unauthorized users.

The configuration of your grid, however, is very much up to you. Based on the example descriptor files (*.xml) and configuration files (*.cfg), it is possible to develop OMERO.grid installations completely tailored to your computing resources.

The whole grid can be shutdown by stopping the master node via: omero admin stop. Each individual node can also be shutdown via: omero node NAME stop on that particular node.

Deployment examples

Two examples will be presented showing the flexibility of OMERO.grid deployment and identifying files whose modification is critical for the deployment to work.

Nodes on a single host

The first example will focus on changing the deployed nodes/servers on a single host. It should serve as an introduction to the concepts. Unless used for very specific requirements, this type of deployment doesn’t yield any performance gains.

The first change that you will want to make to your application descriptor is to add additional processors. Take a look at https://github.com/ome/openmicroscopy/blob/develop/etc/templates/grid/default.xml. There you can define two new nodes - node1 and node2 by simply adding a new XML element below the master node definition:

<node name="node1">
  <server-instance template="ProcessorTemplate" index="1"/>
</node>

<node name="node2">
  <server-instance template="ProcessorTemplate" index="2"/>
</node>

Remember to change the node name and the index number for each subsequent node definition. The node name and the index number do not need to match. In fact, the index number can be completely ignored, except for the fact that it must be unique. The node name, however, is important for properly starting your new processor.

You will need both a configuration file under etc/ with the same name, and unless the node name matches the name of your local host, you will need to specify it on the command line:

omero node node1 start

or with the environment variable OMERO_NODE:

OMERO_NODE=node1 omero node start

After starting up both nodes, you can verify that you now have three processors running by looking at the output of omero admin diagnostics.

For more information on using scripts, see the OMERO.scripts advanced topics.

Nodes on multiple hosts

Warning

Before attempting this type of deployment, make sure that the hosts can ping each other and that required ports are open and not firewalled.

A more complex deployment example is running multiple nodes on networked hosts. Initially, the host’s loopback IP address (127.0.0.1) is used in the grid configuration files.

For this example, let’s presume we have control over two hosts: omero-master (IP address 192.168.0.1/24) and omero-slave (IP address 192.168. 0.2/24). The goal is to move the processor server onto another host (omero-slave) to reduce the load on the host running the master node (omero-master). The configuration changes required to achieve this are outlined below.

On host omero-master:

etc/grid/default.xml - remove or comment out from the master node the server-instance using the ProcessorTemplate. Below the master node add an XML element defining a new node:
```
<node name="omero-slave">
  <server-instance template="ProcessorTemplate" index="0" dir=""/>
</node>
```
etc/internal.cfg - change the value of Ice.Default.Locator from 127.0.0.1 to 192.168.0.1
etc/master.cfg - change all occurrances of 127.0.0.1 to 192.168.0.1

On host omero-slave:

copy or rename etc/node1.cfg to etc/omero-slave.cfg and change all node1 strings to omero-slave in etc/omero-slave.cfg. Also update the IceGrid.Node.Endpoints value to tcp -h 192.168.0.2
etc/internal.cfg - change the value of Ice.Default.Locator from 127.0.0.1 to 192.168.0.1
etc/ice.config - add the line Ice.Default.Router=OMERO.Glacier2/router:tcp -p 4063 -h 192.168.0.1

To apply the changes, start the OMERO instance on the omero-master node by using omero admin start. After that, start the omero-slave node by using omero node omero-slave start. Issuing omero admin diagnostics on the master node should show a running processor instance and the omero-slave node should accept job requests from the master node.

Securing grid resources

More than just making sure no malicious code enters your grid, it is critical to prevent unauthorized access via the application descriptors (*.xml) and configuration (*.cfg) as mentioned above.

Firewall

The simplest and most effective way of preventing unauthorized access is to have all OMERO.grid resources behind a firewall. Only the Glacier2 router has a port visible to machines outside the firewall. If this is possible in your configuration, then you can leave the internal endpoints unsecured.

SSL

Though it is probably unnecessary to use transport encryption within a firewall, encryption from clients to the Glacier2 router will often be necessary. For more information on SSL, see SSL.

Permissions Verifier

The IceSSL plugin can be used both for encrypting the channel as well as authenticating users. SSL-based authentication, however, can be difficult to configure especially for within the firewall, and so instead you may want to configure a “permissions verifier” to prevent non-trusted users from accessing a system within your firewall. From master.cfg:

IceGrid.Registry.AdminPermissionsVerifier=IceGrid/NullPermissionsVerifier
#IceGrid.Registry.AdminCryptPasswords=etc/passwd

Here we have defined a “null” permissions verifier which allows anyone to connect to the registry’s administrative endpoints. One simple way of securing these endpoints is to use the AdminCryptPasswords property, which expects a passwd-formatted file at the given relative or absolute path:

mrmypasswordisomero TN7CjkTVoDnb2
msmypasswordisome   jkyZ3t9JXPRRU

where these values come from using openssl:

$ openssl
OpenSSL> passwd
Password:
Verifying - Password:
TN7CjkTVoDnb2
OpenSSL>

Another possibility is to use the OMERO.blitz permissions verifier, so that anyone with a proper OMERO account can access the server.

See Controlling Access to IceGrid Sessions of the Ice manual for more information.

Unique node names

Only a limited number of node names are configured in an application descriptor. For an unauthorized user to fill a slot, they must know the name (which is discoverable with the right code) and be the first to contact the grid saying “I am Node029”, for example. A system administrator need only then be certain that all the node slots are taken up by trusted machines and users.

It is also possible to allow “dynamic registration” in which servers are added to the registry after the fact. In some situations this may be quite useful, but is disabled by default. Before enabling it, be sure to have secured your endpoints via one of the methods outlined above.

Absolute paths

The example application descriptors shipped with OMERO all use relative paths to make installation easier. Once you are comfortable with configuring OMERO.grid, it would most likely be safer to configure absolute paths. For example, specifying that nodes execute under /usr/lib/omero requires that whoever starts the node have access to that directory. Therefore, as long as you control the boxes which can attach to your endpoints (see Firewall), then you can be relatively certain that no tampering can occur with the installed binaries.

Technical information and other tips

Processes

It is important to understand just what processes will be running on your servers. When you run omero admin start, icegridnode is executed which starts a controlling daemon and deploys the proper descriptor. This configuration is persisted under var/master and var/registry.

Once the application is loaded, the icegridnode daemon process starts up all the servers which are configured in the descriptor. If one of the processes fails, it will be restarted. If restart fails, eventually the server will be “disabled”. On shutdown, the icegridnode process also shutdowns all the server processes.

Targets

In application descriptors, it is possible to surround sections of the description with <target/> elements. For example, in templates.xml the section which defines the main OMERO.blitz server includes:

<server id="Blitz-${index}" exe="${JAVA}" activation="always" pwd="${OMERO_HOME}">
  <target name="debug">
    <option>-Xdebug</option>
    <option>-Xrunjdwp:server=y,transport=dt_socket,address=8787,suspend=y</option>
  </target>
  ...

When the application is deployed, if “debug” is added as a target, then the -Xdebug, etc. options will be passed to the Java runtime. This will allow remote connection to your server over the configured port.

Multiple targets can be enabled at the same time:

omero admin deploy etc/grid/default.xml debug secure someothertarget

Ice.MessageSizeMax

Ice imposes an upper limit on all method invocations. This limit, Ice.MessageSizeMax, is configured in your application descriptor (e.g. templates.xml) and configuration files (e.g. ice.config). The setting must be applied to all servers which will be handling the invocation. For example, a call to InteractiveProcessor.execute(omero::RMap inputs) which passes the inputs all the way down to processor.py will need to have a sufficiently large Ice.MessageSizeMax for: the client, the Glacier2 router, the OMERO.blitz server, and the Processor.

The default is currently set to 65536 kilobytes which is 64MB.

Logging

Currently all output from OMERO.grid is stored in $OMERO_PREFIX/var/log/master.out with error messages going to $OMERO_PREFIX/var/log/master.err. Individual services may also create their own log files.

Shortcuts

If the omero script is copied or symlinked to another name, then the script will separate the name on hyphens and execute omero with the second and later parts prepended to the argument list.

For example,

ln -s omero omero-admin
omero-admin start

works identically to:

omero admin start

Symbolic linking

Shortcuts allow the bin/omero script to function as an init.d script when named omero-admin, and need only be copied to /etc/init.d/ to function properly. It will resolve its installation directory, and execute from there.

For example,

ln -s $VENV_SERVER/bin/omero /usr/local/bin/omero
omero-admin start

The same works for putting bin/omero on your path:

PATH=$VENV_SERVER/bin:$PATH

This means that OMERO.grid can be unpacked anywhere, and as long as the user invoking the commands has the proper permissions on the $OMERO_PREFIX directory, it will function normally.

Running as root

One exception to this rule is that starting OMERO.grid as root may actually delegate to another user, if the “user” attribute is set on the <server/> elements in etc/grid/templates.xml.