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Example production server set-ups

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Groups and permissions system

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Known limitations

Java issues

OpenJDK8 is not currently supported, however OracleJDK8 is supported. OpenJDK and OracleJDK versions 6 and 7 are also supported.

Windows OS issues

UTF-8 character limitations in passwords

Windows does not handle non-Latin characters well in the command prompt (console). If you use Unicode characters in your passwords, you may find they are not correctly formed. Therefore, we recommend you avoid them if at all possible.

OMERO.web ‘development server’ does not work under Windows XP

The development server included with OMERO.web does not work under Windows XP. This server is included to allow you to easily evaluate and develop the OMERO.web component. As it should not be used in a production environment, while an inconvenience, this should not stop the deployment of a production version of OMERO.web. See OME forum topic.

Binary delete

On Windows servers not all binary files corresponding to a delete may be removed from the binary repository. See Binary data for more details.

Mac OS X issues

C++ compilation problems on Mac OS X 10.6 (Snow Leopard)

Under certain circumstances building OmeroCpp can fail with “ld: symbol(s) not found”. You can find further details, a potential solution and make any comments on your experience with the problem on #3210.

Ubuntu issues

Importing using desktop clients

Under older Ubuntu installations, the ‘import folder’ option in the desktop clients currently does not work.

Too many open file descriptors

Starting with OMERO 5, the server works directly from original files. At times, this requires a significant number of open file handles. If you are having problems with large or frequent imports, are seeing “Too many open file descriptors” or similar, you may need to increase the maximum number of open files per process. On Linux, this may be done by setting the nofile limit in /etc/security/limits.conf, for example:

omero  soft  nofile  10000
omero  hard  nofile  12000

This permits the omero user to have 10000 open files per process, which may be increased up to a maximum of 12000 by the user. The username and limits will need adjusting for the specifics of your installation and usage requirements. Note that these settings take effect only for new logins, so the server and the shell or environment the server is started from will require restarting. Run ulimit -a as the user running OMERO to verify that the changes have taken effect.

Deleting datasets

If you have a dataset containing any images which are also present in any other datasets, you will not be able to delete it. First, you must remove the shared images by cutting the links.

Changing group permissions

If you have data which has been linked by other users, you cannot make the group that data is in into a private group.

File format support

DeltaVision OMX files (.hdr) not viewable

Some files generated by an OMX system have a pixel type of float and a large dynamic range. While the files import into OMERO they are currently not viewable. This fix would require deep changes to several parts of the code and we have chosen not to make the changes yet. See #3256.


Enabling synchronization of LDAP on user login will result in LDAP being treated as the authority on both group membership and also the available groups. Any groups defined in OMERO and not in LDAP will result in users being removed from these groups. The groups will still exist in OMERO but user membership will be treated as being defined by LDAP alone.