[ome-users] need help with the OMERO upgrade to OMERO 4.2.0 on a Mac server
Josh Moore
josh.moore at gmx.de
Thu Aug 19 08:38:37 BST 2010
Hi Ron,
in Blitz-0.log, this failure is shown:
Caused by: org.postgresql.util.PSQLException: Connection refused. Check that the hostname and port are correct and that the postmaster is accepting TCP/IP connections.
at org.postgresql.core.v3.ConnectionFactoryImpl.openConnectionImpl(ConnectionFactoryImpl.java:123)
at org.postgresql.core.ConnectionFactory.openConnection(ConnectionFactory.java:66)
at org.postgresql.jdbc2.AbstractJdbc2Connection.<init>(AbstractJdbc2Connection.java:124)
at org.postgresql.jdbc3.AbstractJdbc3Connection.<init>(AbstractJdbc3Connection.java:30)
at org.postgresql.jdbc3.Jdbc3Connection.<init>(Jdbc3Connection.java:24)
at org.postgresql.Driver.makeConnection(Driver.java:386)
at org.postgresql.Driver.connect(Driver.java:260)
at bitronix.tm.resource.jdbc.lrc.LrcXADataSource.getXAConnection(LrcXADataSource.java:79)
... 100 more
Is it possible that PostgreSQL is not listening for TCP connections? See the "Checking PostgreSQL port listening status" section of "OMERO and PostgreSQL":
https://www.openmicroscopy.org/site/support/omero4/server/postgresql#section-2
If that's not the problem, what are the configuration values for "omero.db.host" and "omero.db.port" from `bin/omero config`? If empty, they default to "localhost" and "5432", which judging from your pg_ctl line is most likely correct.
Cheers,
~Josh.
On Aug 18, 2010, at 12:09 AM, Taylor, Ronald C wrote:
>
> 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
> <Blitz-0.log><DropBox.log><FileServer.log><Indexer-0.log><master.err><MonitorServer.log><Processor-0.log><Tables-0.log>_______________________________________________
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