Troubleshooting an OMERO Installation

Remote clients can't connect to my OMERO installation!

The OMERO WebAdmin appears to work fine and you may or may not have created some users but no matter what you do remote clients won't speak to OMERO. OMERO.insight gives you an error message similar to the following (and you know that you've put the correct username and password into the OMERO.insight dialog):

This because of a common /etc/hosts misconfiguration on the machine that runs your OMERO server which affects the ability of remote clients to locate it.

For example if the network name of your OMERO server machine is my-hostname on the network domain lifesci.example.com with IP address 192.168.0.100 then you may have:

# /etc/hosts: Local Host Database
#
# This file describes a number of aliases-to-address mappings for the for 
# local hosts that share this file.
#
# In the presence of the domain name service or NIS, this file may not be 
# consulted at all; see /etc/host.conf for the resolution order.
#

# IPv4 and IPv6 localhost aliases - SHOWING INCORRECT SETUP
127.0.0.1       my-hostname.lifesci.example.com my-hostname localhost
::1             localhost

The offending line here is:

127.0.0.1       my-hostname.lifesci.example.com my-hostname localhost

In order for your OMERO.server installation to function correctly, the correct IP address (not 127.0.0.1) must be specified in /etc/hosts as follows:

127.0.0.1       localhost
192.168.0.100   my-hostname.lifesci.example.com my-hostname

After this change has been completed you must restart your OMERO server.

MBEANS THAT ARE THE ROOT CAUSE OF THE PROBLEM or BEAN exceptions spew forth on the JBoss console and/or in your server.log

1. Check that you are able to successfully connect to your PostgreSQL installation as outlined on the OmeroAndPostgres page.
2. Check the permissions on your omero.data.dir (/OMERO by default) as outlined on the OmeroInstall page, in the Pre-Installation section.

Connection Problems and TCP Window Scaling

Later versions of the 2.6 Linux kernel, specifically 2.6.17, have TCP window scaling enabled by default. If you're 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

You can read more about the problems surrounding TCP window scaling here.

My 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 the SSH session you will use to start OMERO.server by using the -x flag as follows:

ssh -x my_server.examples.com

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 for more information.

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See also: OmeroCommunity, OmeroInstall, OmeroAndPostgres