Known limitations
=================
Time zone
---------
We do not recommend changing the time zone on your server. The server is
currently set to use local time and changing time zones will result in a
mismatch between the original data import times stored in the server and the
way the clients report them. A fix for this is forthcoming but will not be in
5.1.
Java issues
-----------
OpenJDK8 is supported, however some builds of some releases (such as
the current Ubuntu build of 8u40) have broken JPEG support, reported
for `OpenJDK
<http://icedtea.classpath.org/bugzilla/show_bug.cgi?id=1393>`__ and
`Ubuntu
<https://bugs.launchpad.net/ubuntu/+source/openjdk-8/+bug/1421501>`__.
OracleJDK8 is also supported, but the earliest releases have had
problems. The latest OpenJDK8 or OracleJDK8 should work
correctly. OpenJDK and OracleJDK versions 6 and 7 are also supported.
Windows OS issues
-----------------
Django 1.8 will not work with IIS on Windows
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
OMERO.web has been upgraded to use Django 1.8 but support for deploying it
using IIS on Windows is still upcoming and you must use Django 1.6 for now. We
aim to add support for Django 1.8 in OMERO.web within the 5.2.x development
line.
.. _windows-database-encoding:
Failure response on import for new databases
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
If you have import failures with an error such as::
java.lang.RuntimeException: Failure response on import!
Category: ::omero::grid::ImportRequest
Name: import-request-failure
Parameters: {stacktrace=java.lang.RuntimeException: omero.ValidationException
serverStackTrace = "ome.conditions.ValidationException: could not
insert: [ome.model.core.Pixels]; SQL [insert into pixels (creation_id,
external_id, group_id, owner_id, permissions, update_id,
dimensionOrder, methodology, physicalSizeXUnit, physicalSizeX,
physicalSizeYUnit, physicalSizeY, physicalSizeZUnit, physicalSizeZ,
pixelsType, relatedTo, sha1, significantBits, sizeC, sizeT, sizeX,
sizeY, sizeZ, timeIncrementUnit, timeIncrement, version, waveIncrement,
waveStart, image, image_index, id) values (?, ?, ?, ?, ?, ?, ?, ?, ?,
?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)];
nested exception is org.hibernate.exception.DataException: could not
insert: [ome.model.core.Pixels]
when trying to import data to a new database (or possibly one just upgraded to
5.1), it may be an issue with the language encoding during database
initialization leading to corrupted Unicode characters, such that any import
containing these characters (e.g. µ) will fail with the above exception. A
``SET CLIENT_ENCODING TO 'UTF8';`` command has been added to the database
initialization instructions on :doc:`windows/server-installation` to prevent
this.
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 :forum:`OME forum
topic <viewtopic.php?f=5&t=640>`.
Binary delete
^^^^^^^^^^^^^
On Windows servers not all binary files corresponding to a delete may
be removed from the binary repository. See :ref:`DeleteBinaryData` 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 :ticket:`3210`.
Ubuntu issues
-------------
Importing using desktop clients
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Under older Ubuntu installations, the 'import folder' option in the desktop
clients currently does not work.
Windows issues
--------------
C++ compilation problems
^^^^^^^^^^^^^^^^^^^^^^^^
OMERO.cpp will not currently build on Windows due to exceeding DLL
symbol limits on this platform, leading to a failure when linking
the DLL. It is hoped that this platform limitation can be worked
around in a future OMERO release.
Searching
---------
.. _limitations-openfiles:
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 :file:`/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
-------------------
Large images with floating-point pixel data
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Pyramids of image tiles are currently not generated for images with
floating-point pixel data, meaning the imported image will be scrambled if it
is over a certain size (configurable using
:property:`omero.pixeldata.max_plane_height` and
:property:`omero.pixeldata.max_plane_width` but set to 3192x3192 pixels by
default). This primarily affects the following file formats:
* Gatan DM3
* MRC
* TIFF
.. _minmax_limitation:
Calculation of minima and maxima pixel values
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
If images are imported with one of the :option:`omero import --skip` options
skipping calculation of the global minima and maxima pixel values, OMERO
clients will use the extrema of the pixel type range by default. Users can
adjust the minima/maxima via the rendering settings. Recalculating minima and
maxima pixel values after import is currently not supported.
Flex data in OMERO.tables
^^^^^^^^^^^^^^^^^^^^^^^^^
If you are using the advanced configuration setting ``FlexReaderServerMaps``
for importing Flex data split between multiple directories for use with
:doc:`OMERO.tables </developers/analysis>`, you should not upgrade to 5.1.0.
LDAP
----
Enabling synchronization of LDAP on user login may override admin actions
carried out in the clients, see :ref:`synchronizing-ldap` for details.