OMERO.server installation ========================= This section covers the installation of OMERO.server on UNIX and UNIX-like platforms. This includes all BSD, Linux and Mac OS X systems. Depending upon which platform you are using, you may find a more specific walk-through listed below. .. seealso:: :doc:`server-centos6` Instructions for installing OMERO.server from scratch on CentOS 6 with Python 2.7 and Ice 3.5. :doc:`server-centos6-ice36` Instructions for installing OMERO.server from scratch on CentOS 6 with Python 2.7 and Ice 3.6. :doc:`server-centos7` Instructions for installing OMERO.server from scratch on CentOS 7 with Ice 3.5. :doc:`server-centos7-ice36` Instructions for installing OMERO.server from scratch on CentOS 7 with Ice 3.6. :doc:`server-linux-walkthrough` Instructions for installing OMERO.server from scratch on Ubuntu 14.04 with Ice 3.5. :doc:`server-ubuntu1404-ice36` Instructions for installing OMERO.server from scratch on Ubuntu 14.04 with Ice 3.6. :doc:`server-install-homebrew` Instructions for installing and building OMERO.server on Mac OS X with Homebrew using our special formulas (i.e. from the source code via Homebrew). **You do not need to refer to this page to install the prerequisites with Homebrew and then install the server zip from the downloads page.** Prerequisites ------------- Installation will require: - a clean, minimal operating system installation - a "root" level account for which you know the password .. note:: If you are unsure of what it means to have a "root" level account, or if you are generally having issues with the various users/passwords described in this install guide, please see :ref:`troubleshooting-password`. The installation and configuration of the prerequisite applications are mostly outside the scope of this document. For Linux distributions, use of the default package manager is recommended. For BSD systems, the ports system provides all the prerequisites. For MacOS X, Homebrew is recommended. This guide provides the package names to install for a number of contemporary systems. However, the names and versions provided vary between releases. Please do check for similar packages if the one documented here is not available for your system as it may be provided under an alternative name. "Debian" refers to Debian and derivative distributions such as Ubuntu. "RedHat" refers to RedHat and related distributions such as CentOS, Fedora and Scientific Linux. * For Ubuntu you need to enable the **universe** repository. This should be enabled by default. If not enabled, it may be enabled by editing :file:`/etc/apt/sources.list` directly, in which case the entries may already exist but are commented out, or by using Synaptic (10.04 and 10.10) or Ubuntu Software Center (11.04 onwards). Update your package lists to ensure that you get the latest packages:: $ sudo apt-get update Install packages by running:: $ sudo apt-get install package where *package* is the package name to install. .. _server-requirements: The following subsections cover the details for each package, in the order recommended for installation. Java SE Runtime Environment (JRE) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ If possible, install one of the following packages: +-----------+---------------------------+ | System | Package | +===========+===========================+ | BSD Ports | java/openjdk7 | +-----------+---------------------------+ | Debian | openjdk-7-jre | +-----------+---------------------------+ | Homebrew | N/A (install Oracle Java) | +-----------+---------------------------+ | RedHat | java-1.8.0-openjdk | +-----------+---------------------------+ OMERO works with the OpenJDK JRE provided by most systems, or with Oracle Java. Version 7 or later is recommended. Your system may already provide a suitable JRE, in which case no extra steps are necessary. Linux distributions usually provide OpenJDK, and older MacOS X versions have Java installed by default. Oracle Java is no longer provided by BSD or Linux distributions for licensing reasons. If your system does not have Java available, for example on newer MacOS X versions, or the provided version is too old, Oracle Java may be downloaded from the `Oracle website `_. .. warning:: **Security** Installing Oracle Java outside the system's package manager will leave your system without regular distribution-supplied security updates, and so is not recommended. To check which version of Java is currently available:: $ which java /usr/bin/java $ java -version java version "1.7.0_51" Java(TM) SE Runtime Environment (build 1.7.0_51-b13) Java HotSpot(TM) 64-Bit Server VM (build 24.51-b03, mixed mode) Python 2 ^^^^^^^^ Check you have Python (and check its version) by running: :: $ python --version Python 2.7.10 .. note:: OMERO does not currently support Python 3; you must use 2.7. The following Python packages are required: .. tabularcolumns:: |l|l|l| .. list-table:: :header-rows: 1 * - Package - Functionality - Downloads * - `Django`_ (1.8) [1]_ - OMERO.web - :pypi:`Django` page * - `Pillow`_ [2]_ - OMERO.web and Figure Export - :pypi:`Pillow` page * - Matplotlib_ - OMERO.web - `Matplotlib page `_ * - NumPy (1.2.0 or higher) [3]_ - Scripting - `Numpy/Scipy page `_ * - PyTables (2.1.0 or higher) - :doc:`OMERO.tables ` - `PyTables page `_ .. [1] The currently supported version of the django module used by OMERO.web (1.8) requires Python 2.7. The older version (1.6) will work with Python 2.6 but lacks security support, and is consequently *not recommended for production use*. Python 2.7 and `Django 1.8`_ are required for security support. .. [2] Make sure to have `libjpeg `_ installed when building `Pillow`_. We currently do not support version 3.0+. .. [3] May already have been installed as a dependency of Matplot Lib. .. note:: Some of these can be ignored if you wish to forego some functionality but we recommend you just install everything. For example, scripting is enabled by default so should not be assumed optional even if you never expect your users to run scripts from the clients. If possible, install the following packages: .. tabularcolumns:: |l|l| .. list-table:: :header-rows: 1 :widths: 1,8 * - System - Package * - BSD Ports - lang/python27 graphics/py-pillow math/py-matplotlib math/py-numpy devel/py-tables science/py-scipy * - Debian - python2.7 python-pil python-matplotlib python-numpy python-tables python-scipy * - Homebrew - python pillow numpy matplotlib * - RedHat - python .. note:: CentOS 6 users should read :doc:`server-centos6` or :doc:`server-centos6-ice36` and follow the instructions there to install Python and the required modules. Ice ^^^ .. note:: OMERO |version| supports 3.5 and 3.6 on UNIX and UNIX-like platforms. You must install the correct version of OMERO.server (see :downloads:`Downloads <>`). The Ice version may vary, depending upon the distribution version you are using. The Ice versions in currently supported versions of Debian and `Ubuntu `_ are shown in the :ref:`ice-requirements` of the :doc:`/sysadmins/version-requirements` page. Using the latest version of Ice is recommended, where possible. If your package manager provides Ice packages, using these is recommended where possible. Distribution-provided packages often have additional bugfixes which are not present in the upstream releases. If needed, source and binary packages are available from ZeroC_. The latest release is available from the :zeroc:`ZeroC website `. .. note:: CentOS 6 users should read :doc:`server-centos6` or :doc:`server-centos6-ice36` and follow the instructions there to install Ice. .. note:: ZeroC_ Ice can always be built from source code for specific platforms if a binary package is not available. .. note:: With Ice 3.6, the Python bindings are provided separately. If your package manager does not provide Ice python packages, run ``pip install zeroc-ice`` to install the Ice Python bindings. See `Using the Python Distribution `__ for further details. OMERO.web ^^^^^^^^^ Please install one of :program:`apache` (and its wsgi module) or :program:`nginx` and Gunicorn in order to run OMERO.web. +-----------+--------------------------------------+ | System | Packages | +===========+======================================+ | BSD Ports | www/apache24 www/nginx | +-----------+--------------------------------------+ | Debian | apache2 libapache2-mod-wsgi nginx | +-----------+--------------------------------------+ | Homebrew | nginx | +-----------+--------------------------------------+ | RedHat | httpd mod_wsgi nginx | +-----------+--------------------------------------+ OMERO.scripts ^^^^^^^^^^^^^ If you wish to run the "Movie Maker" script, please install :program:`mencoder`. +-----------+---------------------+ | System | Packages | +===========+=====================+ | BSD Ports | multimedia/mencoder | +-----------+---------------------+ | Debian | mencoder | +-----------+---------------------+ | Homebrew | mplayer | +-----------+---------------------+ | RedHat | mencoder | +-----------+---------------------+ Installation ------------ Once the above prerequisites have been downloaded, installed and configured appropriately, the OMERO server itself may be installed. You may wish to create a user account solely for the purpose of running the server, and switch to this user for the next steps. Server directory ^^^^^^^^^^^^^^^^ Firstly, a directory needs to be created to contain the server. In this case :file:`~/omero` is used as an example:: $ mkdir -p ~/omero Next, change into this directory:: $ cd ~/omero OMERO.server ^^^^^^^^^^^^ The release :file:`OMERO.server.zip` is available from the :downloads:`OMERO downloads <>` page. Download the version matching the version of Ice installed on your system before continuing. Installing a development version from source is also possible. See the :ref:`install_from_source` section for further details. This is not recommended unless you have a specific reason *not* to use a release version. Once you have obtained the OMERO.server zip archive matching the version of Ice installed, unpack it: .. parsed-literal:: $ unzip OMERO.server-|release|-ice35-byy.zip If your system does not provide an :program:`unzip` command by default, install one of the following: +-----------+-----------------+ | System | Package | +===========+=================+ | BSD Ports | archivers/unzip | +-----------+-----------------+ | Debian | unzip | +-----------+-----------------+ | Homebrew | unzip | +-----------+-----------------+ | RedHat | unzip | +-----------+-----------------+ Optionally, give your OMERO software install a short name to save some typing later, to reflect what you set :envvar:`OMERO_PREFIX` to in the :ref:`server_env` section, below: .. parsed-literal:: $ ln -s OMERO.server-|release|-ice35-byy OMERO.server This will also ease installation of newer versions of the server at a later date, by simply updating the link. .. _server_env: Environment variables --------------------- If using distribution-provided packages such as Debian or RPM packages, or via the homebrew or macports package manager, it should not be necessary to set any environment variables. However, if using third-party packages for any required components, several variables may require setting in order for them to function correctly. Please note that the precise details of these environment variables can change as new versions of software are released. There are several methods for setting environment variables; which is most appropriate will depend upon how the OMERO server is started. Options include: :file:`/etc/security/pam_env.conf` Global environment set at login by PAM :file:`/etc/profile` or :file:`/etc/profile.d/omero` Global Bourne shell defaults (also used by derived shells such as :program:`bash` and :program:`zsh`) :file:`~/.profile` User's Bourne shell defaults (also used by derived shells) :file:`/etc/bash.bashrc` Global :program:`bash` defaults :file:`~/.bashrc`, :file:`~/.bash_profile` or :file:`~/.bash_login` User's :program:`bash` configuration. If OMERO is started as a service using an init script, a global setting should be preferred. If being started by hand using a particular user, a user-specific configuration file may be more appropriate. The following environment variables may be configured: :envvar:`LD_LIBRARY_PATH` (Linux) or :envvar:`DYLD_LIBRARY_PATH` (MacOS X) The Ice and PostgreSQL libraries must be on the library search path. If using the packages provided by your distribution, this will already be the case. If using third-party binary distributions the :file:`lib` (or :file:`lib64` if present and using a 64-bit system) directory for each will require adding to the library search path. :envvar:`OMERO_PREFIX` This is not strictly required, but may be set for convenience to point to the OMERO server installation, and is used in this documentation as a shorthand for the installation path. :envvar:`OMERO_TMPDIR` Directory used for temporary files. If the home directory of the user running the OMERO server is located on a slow filesystem, such as NFS, this may be used to store the temporary files on fast local storage. :envvar:`PATH` The search path must include the programs :program:`java`, :program:`python`, :program:`icegridnode` and PostgreSQL commands such as :program:`psql`. If using the packages provided by your distribution, this will already be the case. If using third-party binary distributions such as the ZeroC Ice package, Oracle Java, or PostgreSQL, the :file:`bin` directory for each must be added to the path. The OMERO :file:`bin` directory may also be added to the search path (:file:`${OMERO_PREFIX}/bin` if :envvar:`OMERO_PREFIX` has been set). :envvar:`PYTHONPATH` The Ice :file:`python` directory must be made available to python. If using the Ice packages provided by your distribution, this will already be the case. If using the ZeroC ice package, add the :file:`python` directory to the python path. For Ice 3.6, this should never be required. .. warning:: The :envvar:`OMERO_HOME` environment variable is used internally by OMERO. Unless you really know what you are doing, it is strongly recommended that you do not set this variable (see :doc:`/sysadmins/omero-home-prefix` for details). You can use a different name of your choice instead, indicated by :envvar:`OMERO_PREFIX` in this documentation. After making any needed changes, either source the corresponding file or log back in for them to take effect. Run ``env`` to check them. .. note:: CentOS 6 users should read :doc:`server-centos6` or :doc:`server-centos6-ice36` and set the needed environment variables as documented. Creating a database ------------------- On most systems, a "postgres" user will be created which has admin privileges, while the UNIX ``root`` user itself does *not* have admin privileges. Therefore it is necessary to either become the ``postgres`` user, or use :program:`sudo` as shown below. For the purposes of this guide, the following dummy data is used:: Username: db_user Password: db_password Database: omero_database .. warning:: **Security** These dummy values are examples only and should **not** be used. For a live or public server install these values should be altered to reflect your security requirements---i.e. use your own choice of username and password instead. These should **not** be the same username and/or password as your Linux/Mac/Windows root user! You should also consider restricting access to your server machine, but that is outside the scope of this document. - Create a non-superuser database user and record the name and password used. You will need to configure OMERO to use this username and password later on.:: $ sudo -u postgres createuser -P -D -R -S db_user Enter password for new role: # db_password Enter it again: # db_password - Create a database for OMERO to reside in:: $ sudo -u postgres createdb -E UTF8 -O db_user omero_database - Check to make sure the database has been created, you have PostgreSQL client authentication correctly set up and the database is owned by the **db\_user** user. :: $ psql -h localhost -U db_user -l Password for user db_user: List of databases Name | Owner | Encoding ----------------+----------+----------- omero_database | db_user | UTF8 postgres | postgres | UTF8 template0 | postgres | UTF8 template1 | postgres | UTF8 (4 rows) If you have problems, especially with the last step, take a look at :doc:`server-postgresql` since the authentication mechanism is probably not properly configured. Location for the your OMERO binary repository --------------------------------------------- - Create a directory for the OMERO binary data repository. :file:`/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 which the OMERO.server will use to store binary data. - You can read more about the :doc:`OMERO binary repository `. :: $ sudo mkdir /OMERO - Change the ownership of the directory. :file:`/OMERO` **must** either be owned by the user starting the server (it is currently owned by the system root) or that user **must** have permission to write to the directory. You can find out your username and edit the correct permissions as follows: :: $ whoami omero $ sudo chown -R omero /OMERO Configuration ------------- - Optionally, review :file:`~/omero/OMERO.server/etc/omero.properties`, which contains all default settings. Do not edit this file---it is for reference only. Any configuration settings you would like to change can be changed in the next step. Alternatively, you can view a parsed version of the file under :doc:`/sysadmins/config` or parse it yourself with :omerocmd:`config parse`. - Change any settings that are necessary using :omerocmd:`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 :forum:`link `) :: $ cd ~/omero/OMERO.server $ bin/omero config set omero.db.name 'omero_database' $ bin/omero config set omero.db.user 'db_user' $ bin/omero config set omero.db.pass 'db_password' You can also check the values that have been set using:: $ cd ~/omero/OMERO.server $ bin/omero config get - If you have chosen a non-standard :doc:`OMERO binary repository ` location above, be sure to configure the :property:`omero.data.dir` property. For example, to use :file:`/srv/omero`:: $ omero config set omero.data.dir /srv/omero - Create the OMERO database initialization script. You will need to provide a password for the newly created OMERO root user, either by using the ``--password`` argument or by entering it when prompted. Note that this password is for the root user of the **OMERO.server**, and is not related to the root system user or a PostgreSQL user role. .. parsed-literal:: $ cd ~/omero/OMERO.server $ bin/omero db script --password omero_root_password .. literalinclude:: /downloads/cli/db-script-example.txt .. warning:: **Security** For illustrative purposes, the default password for the OMERO root user is shown as ``omero_root_password``. However, you should **not** use this default values 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 or the database user! - Initialize your database with the script. .. parsed-literal:: $ psql -h localhost -U db_user omero_database < |current_dbver|.sql At this point you should see some output from PostgreSQL as it installs the schema for new OMERO database. - Before starting the OMERO.server, run the OMERO diagnostics script to check that all of the settings are correct, e.g. :: $ bin/omero admin diagnostics - You can now start the server using:: $ bin/omero admin start Creating var/master Initializing var/log Creating var/registry No descriptor given. Using etc/grid/default.xml - If multiple users have access to the system running OMERO you should restrict access to the :file:`OMERO.server/etc` and :file:`OMERO.server/var` directories, for example by changing the permissions on them:: $ chmod 700 ~/omero/OMERO.server/etc ~/omero/OMERO.server/var You should also consider restricting access to the OMERO data repository. The required permissions will depend on whether you are using :doc:`/sysadmins/import-scenarios`. .. note Windows If you would like to move the directory again, see ``bin\winconfig.bat --help``, which gets called automatically on an initial install. - Test that you can log in as "root", either with the OMERO.insight client or on the command-line:: $ bin/omero login Server: [localhost] Username: [root] Password: # omero_root_password You will be prompted for an OMERO username and password. Use the username and password set when running ``bin/omero db script``. JVM memory settings ------------------- The OMERO server starts a number of Java services. Memory settings for these are calculated on a system-by-system basis. An attempt has been made to have usable settings out of the box, but if you can afford to provide OMERO with more memory, it will certainly improve your overall performance. See :ref:`jvm_memory_settings` on how to tune the JVM. OMERO.web and administration ---------------------------- In order to deploy OMERO.web in a production environment such as Apache or Nginx please follow the instructions under :doc:`install-web`. .. note:: The internal Django webserver can be used for evaluation and development. In this case please follow the instructions under :doc:`/developers/Web/Deployment`. Enabling movie creation from OMERO. ----------------------------------- OMERO has a facility to create AVI/MPEG Movies from images. The page :doc:`/sysadmins/omeromovie` details how to enable it. 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 :doc:`backup your database and binary data `. Please do not omit this step. Security ^^^^^^^^ It is also now recommended that you read the :doc:`/sysadmins/server-security` 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 :doc:`/sysadmins/dropbox` or :doc:`/sysadmins/server-ldap`. If you have **Flex data**, you may want to watch :snapshot:`the HCS configuration screencast `. See the :omero_plone:`Feature list ` for more advanced features you may want to use, and :doc:`/sysadmins/config` on how to get the most out of your server. If your users are going to be importing many files in one go, for example multiple plates, you should make sure you set the maximum number of open files to a sensible level (i.e. at least 8K for production systems, 16K for bigger machines). See :ref:`ulimit` for more information. Troubleshooting ^^^^^^^^^^^^^^^ My OMERO install doesn't work! What do I do now? Examine the :doc:`/sysadmins/troubleshooting` page and if all else fails post a message to our :mailinglist:`ome-users` mailing list discussed on the :doc:`/users/community-resources` page. Especially the :ref:`server_fails_to_start` and :ref:`remote_clients_cannot_connect` sections are a good starting point. OMERO diagnostics ^^^^^^^^^^^^^^^^^ If you want help with your server installation, please include the output of the diagnostics command: .. parsed-literal:: $ bin/omero admin diagnostics ================================================================================ OMERO Diagnostics |release| ================================================================================ Commands: java -version 1.7.0 (/usr/bin/java) Commands: python -V 2.7.9 (/usr/bin/python) Commands: icegridnode --version 3.5.1 (/usr/bin/icegridnode) Commands: icegridadmin --version 3.5.1 (/usr/bin/icegridadmin) Commands: psql --version 9.4.5 (/usr/bin/psql) Server: icegridnode running Server: Blitz-0 active (pid = 30324, enabled) Server: DropBox active (pid = 30343, enabled) Server: FileServer active (pid = 30345, enabled) Server: Indexer-0 active (pid = 30348, enabled) Server: MonitorServer active (pid = 30351, enabled) Server: OMERO.Glacier2 active (pid = 30353, enabled) Server: OMERO.IceStorm active (pid = 30376, enabled) Server: PixelData-0 active (pid = 30393, enabled) Server: Processor-0 active (pid = 30394, enabled) Server: Tables-0 inactive (disabled) Server: TestDropBox inactive (enabled) OMERO: SSL port 4064 OMERO: TCP port 4063 Log dir: /home/omero/OMERO.server-5.0.1-ice35-b21/var/log exists Log files: Blitz-0.log 3.0 MB errors=0 warnings=9 Log files: DropBox.log 4.0 KB errors=0 warnings=1 Log files: FileServer.log 0.0 KB Log files: Indexer-0.log 10.0 KB errors=0 warnings=5 Log files: MonitorServer.log 2.0 KB Log files: OMEROweb.log 642.0 KB errors=0 warnings=1 Log files: OMEROweb_request.log 0.0 KB Log files: PixelData-0.log 7.0 KB errors=0 warnings=4 Log files: Processor-0.log 2.0 KB errors=0 warnings=1 Log files: Tables-0.log n/a Log files: TestDropBox.log n/a Log files: master.err 0.0 KB errors=2 warnings=0 Log files: master.out 0.0 KB Log files: Total size 3.83 MB Environment:OMERO_HOME=(unset) Environment:OMERO_NODE=(unset) Environment:OMERO_MASTER=(unset) Environment:OMERO_TEMPDIR=(unset) Environment:PATH=/usr/local/bin:/usr/bin:/bin Environment:ICE_HOME=(unset) Environment:LD_LIBRARY_PATH=(unset) Environment:DYLD_LIBRARY_PATH=(unset) OMERO SSL port:4064 OMERO TCP port:4063 OMERO data dir: '/OMERO' Exists? True Is writable? True OMERO temp dir: '/home/omero/tmp' Exists? True Is writable? True (Size: 0) JVM settings: Blitz-${index} -Xmx621m -XX:MaxPermSize=512m -XX:+IgnoreUnrecognizedVMOptions JVM settings: Indexer-${index} -Xmx414m -XX:MaxPermSize=512m -XX:+IgnoreUnrecognizedVMOptions JVM settings: PixelData-${index} -Xmx621m -XX:MaxPermSize=512m -XX:+IgnoreUnrecognizedVMOptions JVM settings: Repository-${index} -Xmx414m -XX:MaxPermSize=512m -XX:+IgnoreUnrecognizedVMOptions OMERO.web status... You are deploying OMERO.web using apache and mod_wsgi. Cannot check status. Django version: 1.8.7 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 :doc:`/sysadmins/UpgradeCheck` page.