Troubleshooting OMERO ===================== Frequently Asked Questions -------------------------- If you cannot find what you are looking for here, try the :faq_plone:`FAQ <>`. .. _troubleshooting-password: Which user account and password do I use where? ----------------------------------------------- Accounts table, including the example usernames and passwords used in the installation guides: ============ ========================== ========== ============= Account type Function Username Password ============ ========================== ========== ============= System Administrator/Root System (Database) service account postgres System (OMERO) service account omero_user Database Database administrator postgres Database Database user db_user db_password OMERO OMERO administrator root root_password OMERO OMERO users ============ ========================== ========== ============= .. Note:: These example usernames and passwords are provided to help you follow the installation guide examples. Do not use root_password or db_password; substitute your own passwords. There are a total of three types of user accounts: system, database and OMERO accounts. System accounts ^^^^^^^^^^^^^^^ These are accounts on your machine or directory server (e.g. LDAP, Active Directory). One account is used for running the OMERO server (either your own or one you created specially for running OMERO, referred to here as “omero_user”). There is also a user called the "administrator-level user" on the :doc:`Windows installation page ` and "root-level user" on the :doc:`UNIX installation page ` (which includes Mac OS X). A separate “postgres” user is used for running the database server. The “omero_user” account runs the OMERO server, and owns the files uploaded to OMERO. This account must have permission to write to the `/OMERO/` binary repository. Some operations in the install scripts require the root-level/administrator-level privileges in order to use another account to perform particular actions e.g. the “postgres” user to create a database. However **the OMERO.server should never be run as the root-level/administrator-level user or as the system-level “postgres” user**. Database accounts ^^^^^^^^^^^^^^^^^ The PostgreSQL database system contains user and administrative accounts; these are completely separate from the system accounts, above, existing only inside the database. The database administrative user (“postgres”) is the owner of all the database resources, and can create new users internal to the database. A single database account is used at run time by OMERO to talk to your database. Therefore, you must configure the “omero.db.***” values during installation: :: $ bin/omero config set omero.db.user db_user $ bin/omero config set omero.db.pass db_password .. Note:: Do **not** use db_user or db_password here; substitute your own username and password. A database user may have the same name as an account on your machine, in which case a password might not be necessary. OMERO accounts ^^^^^^^^^^^^^^ These accounts only exist inside the OMERO system, and are completely separate from both the system and database accounts, above. The first user which you will need to configure is the “root” OMERO user (different from any root-level Unix account). This is done by setting the password in the database script: .. parsed-literal:: $ bin/omero db script Please enter omero.db.version [OMERO\ |version|\ ]: 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 ~/OMERO\ |version|\ __0.sql Other OMERO users can be created via the OMERO.web admin tool. None of the passwords have to be the same, in fact they should be different **unless you are using the LDAP plugin**. Server fails to start --------------------- 1. Check that you are able to successfully connect to your PostgreSQL installation as outlined on the PostgreSQL page for your OS (:doc:`Windows PostgreSQL page ` or :doc:`UNIX/Mac PostgreSQL page `). 2. Check the permissions on your ``omero.data.dir`` (``/OMERO`` or ``C:\OMERO`` by default) as outlined on the :doc:`unix/server-installation` page for Unix/Mac users, or the :doc:`windows/server-binary-repository` page for Windows users. 3. Are you on a laptop? If you see an error message mentioning :ticket:`"node master couldn't be reached" <7325>`, you may be suffering from a network address swap. Ice does not like to have its network changed as can happen if the server is running on a laptop on wireless. If you lose connectivity to icegridnode, you may have to kill it manually via ``kill PID`` or ``killall icegridnode`` (under Unix). 4. If you see an error message mentioning :ticket:`"Freeze::DatabaseException" <5576>` or :ticket:`"could not lock file: var/registry/\_\_Freeze/lock" <7325>`, your icegrid registry may have become corrupted. This is not a problem, but it will be necessary to stop OMERO and delete the ``var/master`` directory (e.g. ``rm -rf var/master``). When restarting OMERO, the registry will be automatically re-created. Remote clients cannot connect to OMERO installation --------------------------------------------------- The Admin section of OMERO.web appears to work properly and you may or may not have created some users, but no matter what you do remote clients will not speak to OMERO. OMERO.insight gives you an error message similar to the following despite giving the correct username and password: .. figure:: /images/login_failure.png :align: center :width: 35% :alt: Login failure This is often due to firewall misconfiguration on the machine that runs your OMERO server, affecting the ability of remote clients to locate it. Please see the :doc:`/sysadmins/server-security` page. Server crashes with… ---------------------- - ``X11 connection rejected because of wrong authentication`` - ``X connection to localhost:10.0 broken (explicit kill or server shutdown).`` OMERO uses image scaling and processing techniques that may be interfered with when used with |SSH| X11-forwarding. You should disable |SSH| X11-forwarding in your |SSH| session by using the ``-x`` flag as follows before you restart the OMERO.server: :: ssh -x my_server.examples.com OutOfMemoryError / PermGen space errors in OMERO.server logs ------------------------------------------------------------ Out of memory or permanent generation (PermGen) errors can be caused by many things. You may be asking too much of the server. Or you may require an increase in the maximum Java heap or the permanent generation space. This can be done by modifying the IceGrid configuration for your OMERO.server as follows: - In ``etc/grid/templates.xml``: :: … … Replace ``-Xmx512M`` initially with ``-Xmx1024M`` or greater as required, (use ``-Xmx1024M -XX:MaxPermSize=128m`` as an alternative). Furthermore, under certain conditions access of images greater than 4GB can be problematic on 32-bit platforms due to certain bugs within the Java Virtual Machine including `Bug ID: 4724038 `_. A 64-bit platform for your OMERO.server is **HIGHLY** recommended. Import error when running bin/omero ----------------------------------- :: Traceback (most recent call last): File "bin/omero", line 67, in ? import omero.cli ImportError: No module named omero.cli If you get any import related errors while running :file:`bin/omero`, the most likely cause is that your PYTHONPATH is not properly set. - If you installed Ice globally via your package manager, make sure you included ice-python. - If you installed Ice manually, e.g. under ``/opt/Ice-3.3.1`` you need to add ``/opt/Ice-3.3.1/python`` (or similar) to your PYTHONPATH environment variable. See the Ice installation instructions for more information. DropBox fails to start: failed to get session --------------------------------------------- If the main server starts but DropBox fails with the following entry in ``var/log/DropBox.log``, :: 2011-06-07 03:42:56,775 ERROR [ fsclient.DropBox] (MainThread) Failed to get Session: then it may be that the server is taking a relatively long time to start. A solution to this is to increase the number of retries and/or the period (seconds) between retries in ``etc/grid/templates.xml`` :: OMERO.web issues ---------------- OMERO.web is not accessible from remote computer ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ To configure the out-of-the box setup to listen for webadmin and webclient connections on different host run: :: c:\omero_dist> bin/omero web start 'host' 'port' OMERO.web did not start on the production ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ The user opening OMEROweb.log files needs write permissions to the directory containing the log files. So, be sure you have a ``log`` directory with the correct ownership and the path set in ``LOGDIR`` matches the log directory. - In your ``/home/omero/omero_dist/var/lib/`` directory add the following to your ``custom_settings.py`` file: - LOGDIR :: LOGDIR = '/home/omero/weblog/' - Check if ``/home/omero/omero_dist/var/lib/custom_settings.py`` exists. - Check who owns the log directory and log files: :: $ ls -al /home/omero/weblog/ total 49 drwxr-xr-x 2 apache apache 120 Mar 31 11:29 . drwxr-xr-x 10 apache apache 520 Mar 31 11:29 .. -rw-r--r-- 1 apache apache 23766 Mar 31 11:41 OMEROweb.log -rw-r--r-- 1 apache apache 23978 Mar 31 11:41 OMEROweb.log.2009-03-31 - or create log and database directories with, for example, ``apache_user:apache_group`` ownership: :: mkdir /home/omero/weblog chown apache_user:apache_group /home/omero/weblog OMERO.web piecharts ^^^^^^^^^^^^^^^^^^^ 'Drive space' does not generate pie chart or 'My account' does not show markup picture and crop the picture options. Error message says: 'Piechart could not be displayed. Please check log file to solve the problem'. Please check ``var/log/OMEROweb.log`` for more details. There are a few known possibilities: - 'TclError: no display name and no $DISPLAY environment variable'. Turn off the compilation of TCL support in Matplotlib_. - 'ImportError: No module named Image'. Install `Python Imaging Library`_ (packages should be available for your distribution). Also double check if all of the prerequisites were installed from OMERO.web deployment (:doc:`UNIX instructions ` or :doc:`Windows instructions `). Other issues ------------ Connection problems and TCP window scaling on Linux systems ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Later versions of the 2.6 Linux kernel, specifically 2.6.17, have TCP window scaling enabled by default. If you are having initial logins never timeout or problems with connectivity in general you can try turning the feature off as follows: :: # echo 0 > /proc/sys/net/ipv4/tcp_window_scaling Server or clients print "WARNING: Prefs file removed in background..." ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ :: Nov 12, 2008 3:02:50 PM java.util.prefs.FileSystemPreferences$7 run WARNING: Prefs file removed in background /root/.java/.userPrefs/prefs.xml Nov 12, 2008 3:02:50 PM java.util.prefs.FileSystemPreferences$7 run WARNING: Prefs file removed in background /usr/lib/jvm/java-1.7.0-icedtea-1.7.0.0/jre/.systemPrefs/prefs.xml These warnings (also sometimes listed as ERRORS) can be safely ignored, and are solely related to how Java is installed on your system. See http://bugs.sun.com/bugdatabase/view\_bug.do?bug\_id=4751177 or this :ome-users:`ome-users thread <2009-March/001465.html>` on our mailing list for more information. Too many open files ^^^^^^^^^^^^^^^^^^^ This is caused by the number of opened files exceeding the limit imposed by your operating system. It might be due to OMERO leaking file descriptors; if you are not using the latest version, please upgrade, since a number of bugs which could cause this behavior have been fixed. It is also possible for buggy scripts which do not properly release resources to cause this to occur. To view the current per-process limit, run :: ulimit -Hn which will show the hard limit for the maximum number of file descriptors (-Sn will show the soft limit). This limit may be increased. On Linux, see ``/etc/security/limits.conf`` (global PAM per-user limits configuration); it is also possible to increase the limit in the shell with :: ulimit -n newlimit providing that you are uid 0 (other users can only increase the soft limit up to the hard limit). To view the system limit, run :: cat /proc/sys/fs/file-max On Mac OS X, the standard ulimit will not work properly. There are several different ways of setting the ulimit, depending upon the version of OS X you are using, but the most common are to edit ``sysctl.conf`` or ``launchd.conf`` to raise the limit. However, note that both of these methods change the defaults for every process on the system, not just for a single user or service. Increasing the number of available filehandles via 'ulimit -n' ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ValueError: filedescriptor out of range in select() - this is a known issue in Python versions prior to 2.7.0. See :ticket:`6201` and Python `Issue #3392 `_ for more details.