[ome-users] need help with the OMERO upgrade to OMERO 4.2.0 on a Mac server
Taylor, Ronald C
ronald.taylor at pnl.gov
Tue Aug 17 23:09:55 BST 2010
Hi Chris, everybody,
Just tried to install 4.2.0 on a Mac server running OS X 10.6 and failed. The update procedure appears to work OK, and Postgres starts up OK, but I get an error timeout after 5 minutes when I do
omero admin start
%%%%%%%%%%%%
Here's what I see from the command line:
bash-3.2$ pg_ctl start -D /Postgres/Data -l /Postgres/Logs/logfile -o -i
server starting
bash-3.2$
bash-3.2$ pg_ctl status
pg_ctl: server is running (PID: 1337)
/Postgres/bin/postgres "-D" "/Postgres/Data" "-i"
bash-3.2$
bash-3.2$
bash-3.2$
bash-3.2$ omero admin start
No descriptor given. Using etc/grid/default.xml
Waiting on startup. Use CTRL-C to exit
.............................Failed to startup after 5 minutes
bash-3.2$
%%%%%%%%%%%%%%%%%%%%%
and here is the diagnostics printout:
bash-3.2$ omero admin diagnostics
================================================================================
OMERO Diagnostics Beta-4.2.0-r7571-b29
================================================================================
Commands: java -version 1.6.0 (/usr/bin/java -- 2 others)
Commands: python -V 2.6.1 (/usr/bin/python)
Commands: icegridnode --version 3.3.1 (/Library/Ice/Versions/3.3.1/bin/icegridnode)
Commands: icegridadmin --version 3.3.1 (/Library/Ice/Versions/3.3.1/bin/icegridadmin)
Commands: psql --version 8.3.11 (/Postgres/bin/psql)
Server: icegridnode running
Server: Blitz-0 inactive (disabled)
Server: DropBox inactive (disabled)
Server: FileServer active (pid = 1359, enabled)
Server: Indexer-0 inactive (disabled)
Server: MonitorServer active (pid = 1361, enabled)
Server: OMERO.Glacier2 active (pid = 1362, enabled)
Server: OMERO.IceStorm active (pid = 1363, enabled)
Server: Processor-0 activating (enabled)
Server: Repository-1 error: node `repo' couldn't be reached:
the node is not active
Server: Tables-0 activating (enabled)
Server: TestDropBox inactive (enabled)
Log dir: /Library/Omero/Versions/4.2.0/omero_dist/var/log exists
Log files: Blitz-0.log 39.0 KB errors=2 warnings=3
Log files: DropBox.log 1.0 KB errors=2 warnings=1
Log files: FileServer.log 0.0 KB
Log files: Indexer-0.log 51.0 KB errors=2 warnings=3
Log files: MonitorServer.log 0.0 KB
Log files: OMEROweb.log n/a
Log files: Processor-0.log 29.0 KB errors=8 warnings=56
Log files: Tables-0.log 29.0 KB errors=8 warnings=56
Log files: TestDropBox.log n/a
Log files: master.err 0.0 KB
Log files: master.out 0.0 KB
Log files: Total size 0.15 MB
Environment:OMERO_HOME=(unset)
Environment:OMERO_NODE=(unset)
Environment:OMERO_MASTER=(unset)
Environment:PATH=/Library/Omero/Versions/4.2.0/omero_dist/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin:/Postgres/bin:/Library/Java/Home/bi\
n:/System/Library/Frameworks/JavaVM.framework/Versions/Current/Commands:/Library/Ice/Versions/3.3.1/bin
Environment:ICE_HOME=/Library/Ice/Versions/3.3.1
Environment:LD_LIBRARY_PATH=(unset)
Environment:DYLD_LIBRARY_PATH=/Library/Frameworks/BerkeleyDB/Versions/4.6.21.NC/lib:/Library/Frameworks/expat/Versions/2.0.1/lib:/Library/PostgreSQL/Versio\
ns/8.3.11/lib:/Library/mcpp/Versions/2.7.2/lib:/Library/Ice/Versions/3.3.1/lib:/Library/Frameworks/HDF5/Versions/1.8.4_patch1/lib
bash-3.2$
%%%%%%%%%%%%%
I have attached the log files from the directory
/Library/Omero/Versions/4.2.0/omero_dist/var/log
Don't know what's going wrong - would very much appreciate some guidance.
Ron
-----Original Message-----
From: Taylor, Ronald C
Sent: Monday, August 16, 2010 5:11 PM
To: 'Chris Allan'
Cc: ome-users at lists.openmicroscopy.org.uk; ronald.taylor24 at gmail.com; Taylor, Ronald C
Subject: RE: [ome-users] need help with the OMERO.web server part of the upgrade to OMERO 4.2.0 on a Linux box
Chris,
Got back from vacation today and tried your simple solution. That brought up the Django server and everything appears to work fine now on my Linux box. Thanks. I will now go forward and do the install on our Mac server.
Cheers,
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: Saturday, August 07, 2010 5:19 AM
To: Taylor, Ronald C
Cc: ome-users at lists.openmicroscopy.org.uk; Wiley, Steven; ronald.taylor24 at gmail.com
Subject: Re: [ome-users] need help with the OMERO.web server part of the upgrade to OMERO 4.2.0 on a Linux box
On 7 Aug 2010, at 01:51, Taylor, Ronald C wrote:
>
> Hi Chris, everybody,
Hi Ron,
>
> 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.
Great.
>
> 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%
>
> %%%%%%%%%%%%%
All that is required now is:
bin/omero web start
This will start the Django standalone development server. There is no need to muck about with the IceGrid configuration via "server enable" or "server start", etc.
...snip...
>
> - Ron
-Chris
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