[ome-users] need help with the OMERO.web server part of the upgrade to OMERO 4.2.0 on a Linux box

Taylor, Ronald C ronald.taylor at pnl.gov
Sat Aug 7 01:51:10 BST 2010

Hi Chris, everybody,

Well, I tried an upgrade to 4.2.0 on my Linux desktop. Thought I'd try Linux first, before upgrading on our Mac server. 

Things worked OK in terms of bringing up the basic server - I could install the

 file OK. Started the server up using
 omero admin start

 and (very briefly) tried out today the new beta 4.2.0 clients 

from the file

Those clients could find the new server and locate the image files that I had previously stored in OMERO.

Got one remaining problem - cannot bring up OMERO.web.

I followed the instructions on the upgrade page for creating new custom settings, and the new
 file appeared to get created properly in 


I did not do anything else for OMERO.web. I'm using Django, not Apache, and as I remembered things, nothing else was needed to bring up OMERO.web on the default Django server.


So - I tried starting OMERO.web up like so:

sidney161% omero admin ice

Ice 3.3.1  Copyright 2003-2009 ZeroC, Inc.
>>> server enable Web
error: couldn't find server `Web'
>>> quit

As you can see, "Web" cannot be found


Tried restarting OMERO (thought it might not have read the newly created custom_settings.py file) - that did not work:

sidney162% omero admin stop
Waiting on shutdown. Use CTRL-C to exit

sidney163% omero admin start
No descriptor given. Using etc/grid/default.xml
Waiting on startup. Use CTRL-C to exit

sidney164% omero admin ice
Ice 3.3.1  Copyright 2003-2009 ZeroC, Inc.
>>> server enable Web
error: couldn't find server `Web'
>>> quit


Here's what I get from diagnostics:

sidney165% omero admin diagnostics

OMERO Diagnostics Beta-4.2.0-r7571-b29
Commands:   java -version                  1.6.0     (/msrc/apps/jdk_1.6/bin/java -- 2 others)
Commands:   python -V                      2.6.5     (/sid/Omero/Python/bin/python -- 2 others)
Commands:   icegridnode --version          3.3.1     (/sid/Omero/Ice/Ice-3.3.1/bin/icegridnode)
Commands:   icegridadmin --version         3.3.1     (/sid/Omero/Ice/Ice-3.3.1/bin/icegridadmin)
Commands:   psql --version                 8.3.10    (/sid/Omero/Postgres/8.3/bin/psql)

Server:     icegridnode                    running
Server:     Blitz-0                        active (pid = 22340, enabled)
Server:     DropBox                        active (pid = 22354, enabled)
Server:     FileServer                     active (pid = 22359, enabled)
Server:     Indexer-0                      active (pid = 22367, enabled)
Server:     MonitorServer                  active (pid = 22391, enabled)
Server:     OMERO.Glacier2                 active (pid = 22372, enabled)
Server:     OMERO.IceStorm                 active (pid = 22377, enabled)
Server:     Processor-0                    active (pid = 22390, enabled)
Server:     Repository-1                   error: node `repo' couldn't be reached:
the node is not active
Server:     Tables-0                       inactive (disabled)
Server:     TestDropBox                    inactive (enabled)

Log dir:    /sid/Omero/Omero_install/omero_dist/var/log exists

Log files:  Blitz-0.log                    55.0 KB       errors=2    warnings=18  
Log files:  DropBox.log                    4.0 KB        errors=2    warnings=1   
Log files:  FileServer.log                 0.0 KB       
Log files:  Indexer-0.log                  6.0 KB        errors=0    warnings=18  
Log files:  MonitorServer.log              4.0 KB        errors=6    warnings=2   
Log files:  OMEROweb.log                   0.0 KB       
Log files:  Processor-0.log                2.0 KB        errors=0    warnings=1   
Log files:  Tables-0.log                   n/a
Log files:  TestDropBox.log                n/a
Log files:  master.err                     0.0 KB       
Log files:  master.out                     0.0 KB       
Log files:  Total size                     0.07 MB

Parsing Blitz-0.log:[line:42] => Server restarted <= 
Parsing Blitz-0.log:[line:271] => Server restarted <= 



So - I can use some help. I will be away for a week, so no huge rush, but I will resume trying to finish the upgrade when I get back on Monday Aug 16th, so I would appreciate any suggestions.

Hopefully I have forgot to do something simple, but - don't know what that is.

  - Ron
Ronald Taylor, Ph.D.
Computational Biology & Bioinformatics Group
Pacific Northwest National Laboratory
902 Battelle Boulevard
P.O. Box 999, Mail Stop J4-33
Richland, WA  99352 USA
Office:  509-372-6568
Email: ronald.taylor at pnl.gov

-----Original Message-----
From: Chris Allan [mailto:callan at lifesci.dundee.ac.uk] 
Sent: Friday, August 06, 2010 6:15 AM
To: Taylor, Ronald C
Cc: ome-users at lists.openmicroscopy.org.uk; Jeremy Swan; Arcieri, Kenneth (NIH/NICHD) [V]; Wiley, Steven
Subject: Re: [ome-users] Question regarding upgrade to OMERO 4.2 on a Mac server

On 5 Aug 2010, at 20:24, Taylor, Ronald C wrote:

> Hi folks,

Hi Ron,

> Some of you may remember that I have installed OMERO 4.1 on a Linux desktop and a Mac server (and a Mac laptop) here at PNNL. We now would like to try an upgrade on the Mac server to OMERO ver 4.2.
> So - I have taken a look at the upgrade page at
>     http://openmicroscopy.org/site/support/omero4/server/upgrade
> and the process doesn't seem too bad (particularly since it looks like I don't have to update any of the large number of libs OMERO and OMERO.web needs - install of the libs/underlying software was a major task in the initial install, since all our machines lacked just about everything OMERO needed to run). However, I have seen some emails on the list where people have posted problems as to doing the upgrade to 4.2.

Most of the problems surround the slightly different OMERO.web startup for which we'll be trying to streamline the documentation in the coming days and will be providing more of for 4.2.1.

> Is there anything in particular that I should know about doing the upgrade on a Mac server running under OS 10.6? Are any new libs needed (looks like answer is no, but - reassurance would be welcome).
> Ken, Jeremy - have you done the upgrade on your Mac machines at NIH, and do you have any advice to offer?
>   Cheers,
>    Ron

Happy to help you through.


More information about the ome-users mailing list