OMERO.server installation

See also

OMERO.server upgrade

Instructions for upgrading your OMERO.server installation.

Limitations

Installation will require an “Administrator” level account for which you know the password. If you are unsure of what it means to have an “Administrator” level account, or if you are generally having issues with the various users/passwords described in this install guide, please see Which user account and password do I use where?.

• Unless you are clear on the differences, you should also open all consoles as an administrator to prevent file permission issues.

  

• Installation on Windows XP is not explicitly supported, especially for OMERO.web. Significant testing has taken place on Windows Server 2008 and we recommend this version.

• OMERO does not currently support Ice 3.5 or Python 3.

• OMERO.movie is not supported on Windows at present.

• Spaces in installation path names are not currently supported - do not use spaces in your folder names:

  Note

  The default user paths on Windows usually contain spaces so you will need to ensure the path has no spaces, C:\OMERO.server for example.

• A reboot is required after installing the prerequisites.

Prerequisites

Note

The installation of these prerequisite applications is largely outside the scope of this document.

Do not mix 32bit (x86) and 64bit (amd64) packages - install either all 32bit or all 64bit. Check your JRE as well.

The following are necessary:

Java SE Development Kit (JDK)

Java SE Downloads are available from http://www.oracle.com/technetwork/java/javase/downloads/index.html. JDK 6 and above are supported.

Ice (3.3.x or 3.4.x)

Note

OMERO 4.3 and earlier support only Ice 3.3. You will need to download these from ZeroC’s previous versions section. OMERO 4.4 adds support for Ice 3.4 while keeping support for Ice 3.3. For OMERO.server you will need to pick the appropriate downloads for the version of Ice you have installed locally. The downloads for Ice 3.4 have “ice34” in the zip name.

If you are using precompiled packages of Ice and Python (recommended) you should use the versions specified below. In particular since OMERO does not support Python 3 it will not work with the Ice 3.5 package for Windows. If you have previously installed Ice 3.5 you should uninstall it.

Windows installers of Ice can be found on the ZeroC download page and will be called something like Ice-3.4.2.msi (for Ice 3.4.2). If you plan to develop for C++, be sure to read the instructions on the OMERO C++ language bindings page.

Users have reported that under certain conditions installing Ice in the default location (C:\Program Files) might break the Windows PATH (due to special characters present in the file name). In cases where omero admin diagnostics throws any errors related to unexpected paths with Ice, please consider installing Ice in the root of the partition (e.g. C:\Ice).

Python 2 (2.6 or later)

Ice 3.4.x requires Python 2.6.x. You can download a precompiled version from python.org. As this is the “vanilla” python distribution (no extra libraries), you will need to install further dependencies, making sure to download the correct version (2.6, 32/64-bit) for your Python distribution.

32/64-bit

OMERO has been extensively tested with 32-bit Python on Windows. 64-bit Python should also work though it has not been tested as thoroughly. You can obtain 64-bit precompiled dependencies from http://www.lfd.uci.edu/~gohlke/pythonlibs.

Note

OMERO does not currently support Python 3.

Python for Windows extensions

Python for Windows extensions (PyWin32) is required. The installer is available from the PyWin download page.

The version you need is: pywin32-XXX.win32-pyA.B.exe (or pywin32-XXX.win-amd64-pyA.B.exe for 64-bit Python) where XXX should be the latest release number and A and B stand for the Python version, for example pywin32-218.win32-py2.6.exe.

Additional libraries

The following are optional depending on what services you require:

Package	Functionality	Downloads
Pillow	OMERO.web and Figure Export	Pillow page
Matplotlib	OMERO.web	Matplotlib page
NumPy (1.2.0 or higher) [1]	Scripting	Numpy/Scipy page
PyTables (2.1.0 or higher)	OMERO.tables	PyTables page
scipy.ndimage	Volume Viewer [2]	Numpy/Scipy page

[1]	May already have been installed as a dependency of Matplot Lib.

[2]	Allows larger volumes to be viewed in the Volume Viewer.

PostgreSQL (8.4 or higher)

PostgreSQL has to be installed and configured with PL/pgSQL and to accept TCP connections. PostgreSQL 8.3 and earlier are not supported.

The One click installer can be found on the PostgreSQL Windows download page. You will need the postgres user’s password later in the install.

• You must install PostgreSQL as a service if you want to follow this document; other PostgreSQL installation environments are supported but are outside the scope of this document.

1. Run the downloaded installer:

   

2. You may be prompted for permission to continue with a “user account control” dialog. Click yes to continue.

   

3. The installer will now start.

   

4. Choose the installation directory. The default is fine.

   

5. Choose the data directory. The default is fine, but if you want to keep the data in a specific location, you may choose an alternative location here.

   

6. Enter a password for the special “postgres” system account. OMERO does not use this account, but you will need to remember the password for creating the database, below.

   

7. Enter the port number for PostgreSQL to listen on for incoming connections. The default, 5432, is fine and should not be changed.

   

8. Select the locale. The default here is fine.

   

9. PostgreSQL will now be installed and started.

   

Environment variables

For the prerequisite software to run properly, your PATH and PYTHONPATH environment variables must be configured. If not correctly configured or if you installed any of the prerequisites manually to C:\ice or a similar location, you will need to set the values yourself.

Update your Windows environment variables: (REQUIRES RESTART!)

1. Locate the System control panel page on the Start Menu under Settings ‣ Control Panel, open it and navigate to the Advanced tab (on Windows Vista the dialog will be visible after clicking the Change settings link on the System control panel page):

   

   Advanced System Properties

2. Open the Environment Variables dialog by clicking on the Environment Variables... button of the above dialog:

   

   Environment Variables

3. Edit the existing System environment variable Path and add a new variable pointing to the Ice installation bin directory. At the front of the Path variable also add a new string pointing to the Python installation directory (e.g. C:\Python26). Then add a brand new System environment variable called PYTHONPATH pointing to the Ice installation python location:

   

   When setting the ENV variables, make sure you write in the correct paths. You must have entries for:

   • python (the first PATH entry, e.g. “C:\Python26;%Sys…)
   • icebin (the last PATH entry, e.g. “…;C:\Ice-3.4.2\bin;”)
   • PYTHONPATH pointing to the python folder in the ICE installation (e.g. “C:\Ice-3.4.2\python;”)
   • For 64-bit you will need to use the 64-bit Ice directories, for example “C:\Ice-3.4.2\bin\x64;” and “C:\Ice-3.4.2\python\x64;”.

   Warning

   Remember that the Windows path separator is the semicolon ; and must be appended after every entry.

   Make sure the first inserted ENV PATH entry (the python path) finishes with a semicolon (eg. “C:\Python26;%SystemRoot%…”) otherwise you could corrupt other system applications.

4. Restart your computer. For environment changes to take effect in background services, a restart is unfortunately necessary. See http://support.microsoft.com/kb/821761 for more information.

Creating a database for OMERO

Probably the most important step towards having a working server system is having a properly configured database.

• Create a non-superuser database user (make sure to note down the name and password) using pgAdmin III. You can find pgAdmin III on the Start Menu under Programs ‣ PostgreSQL 9.1 ‣ pgAdmin III:

  1. Double-click on the PostgreSQL 9.1 database (or right- click and choose Connect) and provide your postgres user login password set during the installation, above.

     

     Connect to the database server

     

     Enter password

  2. Right-click on Login Roles and select New Login Role...

     

     New login role

  3. Create a new role and record the name and password. You will need to configure OMERO to use your username and password by setting the omero.db.name and omero.db.pass properties.

     Warning

     For illustrative purposes, the default name and password for the role are db_user and db_password respectively. However, you should not use these default values for your installation but use your own choice of username and password instead.

  

  Setting name of new login role

  

  Setting password of new login role

• Create an omero_database database:

  1. Right-click on Databases and select New Database ...

     

     New database

  2. Create a new database with the Name omero_database and Owner db_user (this may take a few moments)

     

     New database name

• Confirm PL/pgSQL language support in your newly created database

  1. First, go to File ‣ Options select the Browser tab and activate the Languages option:

     

     Options menu

     

     Enable display of installed languages

  2. Navigate back to your database, expand the database’s tree view and finally expand the now available Languages item:

     

     View installed languages

  3. If the plpgsql language is missing, right-click on the Extensions item and select the New extension... option in the menu. Finally, add the plpgsql extension, accepting all defaults. This will add both the extension and the language. In older PostgreSQL versions without extensions, right-click on the Languages item and select the New language... option in the menu. Finally, add the plpgsql language, accepting all defaults.

     

     Add new language

     

     New language name

Location for your OMERO binary repository

See also

OMERO.server binary repository

• Create a directory for the OMERO binary data repository (C:\OMERO is the default location and should be used unless you explicitly have a reason not to and know what you are doing).

• This is not where you want the OMERO application to be installed, it is a separate directory that OMERO.server will use to store binary data:

  C:\mkdir OMERO
  

• Change the ownership of the directory. C:\OMERO must either be owned by the user starting the server or that user must have permission to write to the directory. Please see OMERO.server binary repository for more details.

When performing some operations the clients make use of temporary file storage and log directories. By default these files are stored below the user’s home directory (on Windows C:\Users\<username>) in omero\tmp, omero\log and omero\sessions.

Note

If your home directory is stored on a network (NFS mounted or similar), then file read and write operations occur over the network. This can slow access down. Installing OMERO on a network mapped drive is strongly discouraged.

The OMERO.server also accesses the omero\tmp and omero\log folders of the user account running the server process. As the server makes heavier use of these folders than the clients, if that user’s home folder is stored on a network the server can be slowed down. To get around this for the OMERO.server you can define an OMERO_TEMPDIR environment variable pointing to a temporary directory located on the local file system e.g. C:\tmp\.

Installation

• Download and extract the OMERO.server zip file, and note its location. Below it is referred to as C:\OMERO.server.

• Optionally, review C:\OMERO.server\etc\omero.properties which contains all default settings.

  You will need to open the file with a text editor. Do not edit the file. Any configuration settings you would like to change can be changed in the next step.

• Change any settings that are necessary using bin\omero config, including the name and/or password for the ‘db_user’ database user you chose above or the database name if it is not “omero_database”. (Quotes are only necessary if the value could be misinterpreted by the shell. See link).

  C:\> cd C:\OMERO.server
  C:\OMERO.server\> bin\omero config set omero.db.name omero_database
  C:\OMERO.server\> bin\omero config set omero.db.user db_user
  C:\OMERO.server\> bin\omero config set omero.db.pass db_password
  

• If you have chosen a non-standard OMERO binary repository location above, be sure to configure the omero.data.dir property.

  When using C:\ style file paths it is necessary to “escape” the backslashes. For example:

  C:\> bin\omero config set omero.data.dir C:\\OMERO
  

• Create the OMERO database initialization script. You will be asked for the version of the script which you would like to generate, where both defaults can be accepted. Finally, you will be asked to enter and confirm password for your newly created OMERO root user.

  Warning

  For illustrative purposes, the default password for the OMERO rootuser is root_password. However, you should not use this default value for your installation but use your own choice of password instead.

  This should not be the same password as your Linux/Mac/Windows root user!

  C:\> cd C:\OMERO.server
  C:\OMERO.server> bin\omero db script
  Please enter omero.db.version [OMERO5.0]:
  Please enter omero.db.patch [0]:
  Please enter password for new OMERO root user: # root_password
  Please re-enter password for new OMERO root user: # root_password
  Saving to C:\OMERO.server\OMERO5.0__0.sql
  

  The generated SQL file is found in the folder where you called the “omero db script” command. This could cause a permission denied error in the populate db step if the postgres user cannot access that location. Move the file to a different location or use the -f option.

• Initialize your database with the script.

  1. Launch SQL Shell (psql) from the Start Menu under Programs ‣ PostgreSQL 9.1 ‣ SQL Shell (psql)

     Server [localhost]:
     Database [postgres]: omero_database
     Port [5432]:
     Username [postgres]: db_user
     Password for user db_user:
     Welcome to psql 9.1.4, the PostgreSQL interactive terminal.
     
     Type:  copyright for distribution terms
             h for help with SQL commands
             ? for help with psql commands
             g or terminate with semicolon to execute query
             q to quit
     
     Warning: Console code page (437) differs from Windows code page
              (1252) 8-bit characters might not work correctly. See psql
              reference page "Notes for Windows users" for details.
     

  2. Execute the following to populate your database (the forward slashes are intentional - if you get a permission denied error it is because the path is wrong, not the slashes):

     omero=> \i C:/OMERO.server/OMERO5.0__0.sql
     ...
     ...
     omero=> \q
     

• Before starting the OMERO.server, you should run the OMERO diagnostics script so that you check that all of the settings are correct, e.g.

  C:\OMERO.server\> bin\omero admin diagnostics
  

  The diagnostic tool may say that psql is not found. This should not be a problem but you can fix it by adding its bin folder to the path. For example, C:\Program Files (x86)\PostgreSQL\9.2\bin. Remember to reboot after changing the environment.

• You can now start the server using:

  C:\OMERO.server> bin\omero admin start
  Creating C:\OMERO.server\var\master
  Creating C:\OMERO.server\var\registry
  No descriptor given. Using etc\grid\windefault.xml
  Installing OMERO.master Windows service.
  Successfully installed OMERO.master Windows service.
  Starting OMERO.master Windows service.
  Waiting on startup. Use CTRL-C to exit
  ...
  

  If you have chosen a non-default install directory (other than C:\OMERO.server), the output will look like this:

  C:\OMERO.server> bin\omero admin start
  Found default value: C:\OMERO.server\var\master
  Attempting to correct...
  Converting from C:\OMERO.server to C:\OMERO.server
  Changes made: 6
  No descriptor given. Using etc\\grid\\windefault.xml
  ...
  

• If you would like to move the directory again, see bin\winconfig.bat --help, which gets called automatically on an initial install.

• You can now test that you can log-in as “root”, either with the OMERO.insight client or command-line:

  C:\OMERO.server> bin\omero login
  Server: [localhost]
  Username: [root]
  Password:         # root_password
  

JVM memory settings

To make your server production-ready, you will likely need to increase the JVM memory settings of your application descriptors. This is not done by default since it would prevent starting the server on some sites’ test instance but for production use a setting higher than 512MB is highly recommended.

To increase the JVM memory settings, you need to edit the etc\grid\templates.xml file under the OMERO.server directory.

It is highly recommended to increase the BlitzTemplate default JVM memory settings from -Xmx512M to -Xmx2048M and from XX:MaxPermSize=128m to XX:MaxPermSize=256M in production.

If working with large images generates OutOfMemory exceptions in the varlogPixelData-0.log file, you may consider increasing the PixelDataTemplate default JVM memory settings to -Xmx1024M.

Once you have modified the templates.xml file, restart the server using:

C:\OMERO.server> bin\omero admin restart

See also

http://www.openmicroscopy.org/community/viewtopic.php?f=4&t=7400

Forum thread on PixelData JVM memory settings

Grid configuration

Section of the advanced server configuration documentation describing etcgridtemplates.xml.

OMERO.web and administration

Note

In order to deploy OMERO.web in a production environment such as Apache or IIS please follow the instructions under OMERO.web deployment.

Otherwise, the internal Django webserver can be used for evaluation and development. In this case, you need to turn debugging on, in order that static files can be served by Django:

c:\OMERO.server> bin\omero config set omero.web.application_server development
c:\OMERO.server> bin\omero config set omero.web.debug True
c:\OMERO.server> bin\omero config set omero.web.session_engine "django.contrib.sessions.backends.cache"
c:\OMERO.server> bin\omero config set omero.web.cache_backend "file://C:/windows/temp/"

then start by

c:\OMERO.server> bin\omero web start
Starting django development webserver...
Validating models...
0 errors found

Django version 1.1.1, using settings 'omeroweb.settings'
Development server is running at http://0.0.0.0:4080/
Quit the server with CONTROL-C.

Once you have deployed and started the server you can use your browser to access the OMERO.web interface:

• http://localhost:4080/

  

  OMERO.webadmin login

Post-installation items

Backup

One of your first steps after putting your OMERO server into production should be deciding on when and how you are going to backup your database and binary data. Please do not omit this step.

Security

You should read the Server security and firewalls page to get a good idea as to what you need to do to get OMERO clients speaking to your newly installed OMERO.server in accordance with your institution or company’s security policy.

Advanced configuration

Once you have the base server running, you may want to try enabling some of the advanced features such as OMERO.dropbox or LDAP authentication. If you have *Flex data*, you may want to watch the HCS configuration screencast. See the Feature list for more advanced features you may want to use, and Advanced configuration on how to get the most out of your server.

Update notification

Your OMERO.server installation will check for updates each time it is started from the Open Microscopy Environment update server. If you wish to disable this functionality you should do so now as outlined on the OMERO upgrade checks page.

Troubleshooting

If you encounter a problem which is not addressed by the Troubleshooting OMERO page, you can post a message to our ome-users mailing list as discussed on the Community support page.

Please include the output of the diagnostics command when asking for help with your server installation:

C:\OMERO.server> bin\omero admin diagnostics
================================================================================
OMERO Diagnostics 5.0.0
================================================================================

Commands:   java -version                  1.6.0     (C:\WINDOWS\system32\java.EXE -- 3 others)
Commands:   python -V                      2.6       (C:\Python26\python.EXE)
Commands:   icegridnode --version          3.3       (C:\Ice-3.3.1\bin\x64\icegridnode.EXE -- 2 others)
Commands:   icegridadmin --version         3.3       (C:\Ice-3.3.1\bin\x64\icegridadmin.EXE -- 2 others)
Commands:   psql --version                 8.3       (C:\Program Files (x86)\PostgreSQL\8.3\bin\psql.EXE -- 2 others)

Server:     icegridnode                    running
Server:     Blitz-0                        active (pid = 7704, enabled)
Server:     DropBox                        active (pid = 8008, enabled)
Server:     FSServer                       active (pid = 7088, enabled)
Server:     Indexer-0                      active (pid = 4728, enabled)
Server:     OMERO.Glacier2                 active (pid = 5456, enabled)
Server:     OMERO.IceStorm                 active (pid = 800, enabled)
Server:     Processor-0                    active (pid = 7316, enabled)
Server:     Tables-0                       active (pid = 4420, enabled)
Server:     TestDropBox                    inactive (enabled)
Server:     Web                            inactive (enabled)
Server:     OMERO.master                   active (running as LocalSystem)

Log dir:    C:\hudson\trunk\dist\var\log   exists

Log files:  Blitz-0.log                    10.0 MB       errors=4    warnings=26
Log files:  DropBox.log                    2.0 KB
Log files:  FSServer.log                   1.0 KB
Log files:  Indexer-0.log                  8.0 MB        errors=18   warnings=1870
Log files:  OMEROweb.log                   n/a
Log files:  Processor-0.log                0.0 KB
Log files:  Tables-0.log                   0.0 KB
Log files:  TestDropBox.log                n/a
Log files:  master.err                     0.0 KB
Log files:  master.out                     0.0 KB
Log files:  Total size                     18.94 MB