[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
omero-Beta4.2.0.tar
file OK. Started the server up using
omero admin start
and (very briefly) tried out today the new beta 4.2.0 clients
OMEROinsight_unix.sh
and
importer-gui
from the file
OMERO.clients-Beta4.2.0.linux.zip
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
custom_settings.py
file appeared to get created properly in
/sid/Omero/Omero_install/omero_dist/var/lib/custom_settings.py
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
sidney162%
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%
sidney163% omero admin start
No descriptor given. Using etc/grid/default.xml
Waiting on startup. Use CTRL-C to exit
sidney164%
sidney164% omero admin ice
Ice 3.3.1 Copyright 2003-2009 ZeroC, Inc.
>>>
>>> server enable Web
error: couldn't find server `Web'
>>> quit
sidney165%
%%%%%%%%%%%%%
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 <=
Environment:OMERO_HOME=(unset)
Environment:OMERO_NODE=(unset)
Environment:OMERO_MASTER=(unset)
Environment:PATH=/usr/local/bin:/sid/Omero/Omero_install/omero_dist/bin:/sid/Omero/Postgres/8.3/bin:/sid/Omero/Python/bin:/sid/Omero/Ice/Ice-3.3.1/bin:/msrc/apps/jdk_1.6/bin:/home/rtaylor:/home/rtaylor/bin:/msrc/apps/bin:/msrc/lapps/bin:/msrc/share/bin:/usr/afsws/bin:/usr/afsws/etc:/sbin:/usr/sbin:/usr/bin:/usr/bin/X11:/bin:.
Environment:ICE_HOME=/sid/Omero/Ice/Ice-3.3.1
Environment:LD_LIBRARY_PATH=/sid/Omero/Postgres/8.3/lib:/sid/Omero/Python/lib:/sid/Omero/expat/lib:/sid/Omero/libiconv/lib:/sid/Omero/Ice/Ice-3.3.1/lib:/sid/Omero/Omero_install/omero_dist/lib
Environment:DYLD_LIBRARY_PATH=(unset)
sidney166%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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.
-Chris
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