[ome-users] OMERO upgrade 5.0.8->5.1.4 failed

[Josh Moore]

> Dear all,

Hi Martin,


> I cannot start a freshly installed OMERO 5.1.4 on ubuntu. I followed the
> instructions on
> http://www.openmicroscopy.org/site/support/omero5.1/sysadmins/server-upgrade.html,
> the db upgrade worked fine.
>
> starting omero leads to:
>
> Creating /home/omero/OMERO.server-5.1.4-ice35-b55/var/master
> Initializing /home/omero/OMERO.server-5.1.4-ice35-b55/var/log
> Creating /home/omero/OMERO.server-5.1.4-ice35-b55/var/registry
> No descriptor given. Using etc/grid/default.xml
> Waiting on startup. Use CTRL-C to exit
> .............................
> Failed to startup some components after 300 seconds
> Calling "stop" on remaining components

Your Blitz-0.log has:

***************************************************************************************
Error connecting to database table dbpatch. You may need to bootstrap.
See http://www.openmicroscopy.org/site/support/omero5.1/sysadmins/server-upgrade.html
***************************************************************************************

Something is amiss with OMERO's connection to the database. A couple
of possible causes I can think of are:

 * Is your OMERO configuration still as you expect? Check the output
of `bin/omero config get` to be sure.

 * Can you reach PostgreSQL from the command line? Depending on your
OMERO configuration, you should try something like, `psql -h localhost
-U omero omero`

 * If you *can't* reach PostgreSQL from the command line, has anything
changed recently, e.g. in the PostgreSQL configuration or the
firewall? Modification to pg_hba.conf?

Cheers,
~Josh.



> Thanks
> Martin
>
> ================================================================================
> OMERO Diagnostics 5.1.4-ice35-b55
>
> ================================================================================
>
>
> Commands:   java -version                  1.7.0     (/usr/bin/java)
>
> Commands:   python -V                      2.7.6     (/usr/bin/python)
>
> Commands:   icegridnode --version          3.5.1
> (/usr/bin/icegridnode)
> Commands:   icegridadmin --version         3.5.1
> (/usr/bin/icegridadmin)
> Commands:   psql --version                 9.3.10    (/usr/bin/psql)
>
>
> Server:     icegridnode                    not started
>
> Log dir:    /home/omero/OMERO.server-5.1.4-ice35-b55/var/log exists
>
> Log files:  Blitz-0.log                    54.0 KB       errors=26
> warnings=0
> Log files:  DropBox.log                    1.0 KB        errors=2
> warnings=1
> Log files:  FileServer.log                 0.0 KB
> Log files:  Indexer-0.log                  54.0 KB       errors=35
> warnings=0
> Log files:  MonitorServer.log              0.0 KB
> Log files:  OMEROweb.log                   n/a
> Log files:  PixelData-0.log                54.0 KB       errors=35
> warnings=0
> Log files:  Processor-0.log                15.0 KB       errors=8
> warnings=4
> Log files:  Tables-0.log                   16.0 KB       errors=8
> warnings=4
> Log files:  TestDropBox.log                n/a
> Log files:  master.err                     0.0 KB        errors=0
> warnings=2
> Log files:  master.out                     0.0 KB
> Log files:  Total size                     0.20 MB
>
>
> Environment:OMERO_HOME=(unset)
> Environment:OMERO_NODE=(unset)
> Environment:OMERO_MASTER=(unset)
> Environment:OMERO_USERDIR=(unset)
> Environment:OMERO_TMPDIR=(unset)
> Environment:PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
> Environment:PYTHONPATH=(unset)
> Environment:ICE_HOME=(unset)
> Environment:LD_LIBRARY_PATH=(unset)
> Environment:DYLD_LIBRARY_PATH=(unset)
>
> Cannot list deployed applications.
> OMERO data dir:'/OMERO'                       Exists? True      Is
> writable? True
> OMERO temp dir:'/home/omero/omero/tmp'        Exists? True      Is
> writable? True   (Size: 0)
>
> JVM settings: Blitz                         -Xmx2509m -XX:MaxPermSize=1g
> -XX:+IgnoreUnrecognizedVMOptions
> JVM settings: Indexer                       -Xmx1672m -XX:MaxPermSize=1g
> -XX:+IgnoreUnrecognizedVMOptions
> JVM settings: Pixeldata                     -Xmx2509m -XX:MaxPermSize=1g
> -XX:+IgnoreUnrecognizedVMOptions
> JVM settings: Repository                    -Xmx1672m -XX:MaxPermSize=1g
> -XX:+IgnoreUnrecognizedVMOptions
>
> OMERO.web status... WARNING: FastCGI support is deprecated and will be
> removed in OMERO 5.2. Install Gunicorn and update config.
> [NOT STARTED]
>
>
> --
> Martin Schorb, PhD
>
> Application Engineer, Electron Microscopy Core Facility
>
> EMBL Heidelberg
> Meyerhofstraße 1,
> 69117 Heidelberg, Germany
> +49 6221 387-8253
> martin.schorb at embl.de
>
>
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>
>
>
>
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