Open Microscopy Environment

Hi world,

I have a question about installation of OMERO 4.1: Is't possible to Install OMERO Beta 4.1.0 server on the Linux machine (for example, RHEL 4)?

Many thanks for your help;

HT

Split the post from the Installation documentation.

Yes, it's possible. You will have a lot of manual work to do on RHEL 4. We suggest at least RHEL/CentOS 5.

I've stickied the CentOS 5 example from OMERO 4.1 in this forum. You can find it directly here:

viewtopic.php?f=5&t=22

Well, could you please, tell me where I can find this manual work to do it on RHEL 4?
Thank you cxallan,

I haven't personally done it but you will have to compile your own Python, Ice, SQLite, etc. and install Java and PostgreSQL. It is not a simple process at all on RHEL 4 and there is limited help I can give you directly. We do not have a step-by-step guide for RHEL 4 so you're going to have to strike out on your own I'm afraid.

We'll certainly answer any specific deployment questions you have however.

Dear cxallan,

Thank you for your answer,

I have installed Omero 4.1.0 on RHEL 5. before that, I compiled Ice, SQLite and installed java 1.6 and postrgresql 8.3.

Now, I encounter some difficulties to start Omero server?

Below, the errors messages which I obtain when I launch the server:

1. RHEL 5 release:
-------------------
OMERO$ more /etc/redhat-release
Red Hat Enterprise Linux Server release 5.2 (Tikanga)

2. Omero diagnostics:
-----------------------
OMERO$ bin/omero admin diagnostics
================================================================================
OMERO Diagnostics Beta-4.1.0-r5585-b12
================================================================================

Commands: java -version 1.6.0 (/local/app/ia64/tools/jdk/bin/java -- 2 others)
Commands: python -V 2.4 (/usr/bin/python)
Commands: icegridnode --version 3.3 (/usr/bin/icegridnode)
Commands: icegridadmin --version 3.3 (/usr/bin/icegridadmin)
Commands: psql --version 8.3.8 (/local/app/ia64/tools/postgresql/8.3/bin/psql)

Server: icegridnode running
Server: Blitz-0 inactive (disabled)
Server: DropBox inactive (disabled)
Server: FSServer inactive (disabled)
Server: Indexer-0 inactive (disabled)
Server: OMERO.Glacier2 active (pid = 12124, enabled)
Server: OMERO.IceStorm active (pid = 12090, enabled)
Server: Processor-0 activating (enabled)
Server: Tables-0 inactive (disabled)
Server: TestDropBox inactive (enabled)
Server: Web inactive (enabled)

Log dir: /local/app/noarch/www/OMERO/var/log exists

Log files: Blitz-0.log 81.0 KB errors=4 warnings=4
Log files: DropBox.log 7.0 KB errors=8 warnings=0
Log files: FSServer.log 3.0 KB errors=4 warnings=0
Log files: Indexer-0.log 66.0 KB errors=4 warnings=4
Log files: OMEROweb.log n/a
Log files: Processor-0.log 1.0 MB errors=429 warnings=3009
Log files: Processor-0.log.1 4.0 MB errors=1342 warnings=9388
Log files: Processor-0.log.2 4.0 MB errors=1342 warnings=9393
Log files: Processor-0.log.3 4.0 MB errors=1341 warnings=9394
Log files: Processor-0.log.4 4.0 MB errors=1342 warnings=9388
Log files: Tables-0.log n/a
Log files: TestDropBox.log n/a
Log files: master.err 5.0 KB errors=0 warnings=8
Log files: master.out 0.0 KB
Log files: Total size 21.77 MB


3. Error message on var/log/master.err
--------------------------------------------

Original exception was:
Traceback (most recent call last):
File "lib/python/runTables.py", line 13, in ?
__import__("tables")
ImportError: No module named tables
Nov 23, 2009 4:09:47 PM java.util.prefs.FileSystemPreferences$7 run
WARNING: Prefs file removed in background /local/app/ia64/tools/jdk1.6.0_17/jre/.systemPrefs/prefs.xml
Nov 23, 2009 4:09:47 PM java.util.prefs.FileSystemPreferences$7 run
WARNING: Prefs file removed in background /local/app/ia64/tools/jdk1.6.0_17/jre/.systemPrefs/prefs.xml
11/23/09 16:09:51.436 OMERO.Glacier2: warning: unable to contact permissions verifier `BlitzVerifier@BlitzAdapters'
Reference.cpp:1546: Ice::NoEndpointException:
no suitable endpoint available for proxy `BlitzVerifier -t @ BlitzAdapters'
11/23/09 16:09:51.437 OMERO.Glacier2: warning: unable to contact session manager `BlitzManager@BlitzAdapters'
Reference.cpp:1546: Ice::NoEndpointException:
no suitable endpoint available for proxy `BlitzManager -t @ BlitzAdapters'

Those are expected if you do not have PyTables installed. Nothing to be worried about. If you want to install the pre-requisites of OMERO.tables (a preview feature of OMERO 4.1.0), of which PyTables is a member, you can find out more information here:

http://trac.openmicroscopy.org.uk/omero ... meroTables