Omero server failed to startup


After installing the OMERO server and run the start it shows the error

[omero@cngbdb-d13-11 log]$ omero admin start
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
Waiting on shutdown. Use CTRL-C to exit

Then I diagnostics it

[omero@cngbdb-d13-11 log]$ omero admin diagnostics

OMERO Diagnostics (admin) 5.5.1-ice36-b122

Commands:   java -version                  error:'NoneType' object has no attribute 'group'
Commands:   python -V                      2.7.15    (/usr/local/bin/python -- 2 others)
Commands:   icegridnode --version          3.6.4     (/bin/icegridnode)
Commands:   icegridadmin --version         3.6.4     (/bin/icegridadmin)
Commands:   psql --version                 9.4.23    (/bin/psql)
Commands:   openssl version                1.0.2     (/bin/openssl)

Server:     icegridnode                    not started

Log dir:    /home/omero/OMERO.server/var/log exists
Log files:  Blitz-0.log                    109.0 KB      errors=6    warnings=9
Log files:  DropBox.log                    4.0 KB        errors=6    warnings=3
Log files:  FileServer.log                 1.0 KB
Log files:  Indexer-0.log                  75.0 KB       errors=3    warnings=3
Log files:  MonitorServer.log              1.0 KB
Log files:  PixelData-0.log                75.0 KB       errors=3    warnings=3
Log files:  Processor-0.log                45.0 KB       errors=13   warnings=26
Log files:  Tables-0.log                   n/a
Log files:  TestDropBox.log                n/a
Log files:  master.err                     95.0 KB       errors=3    warnings=6
Log files:  master.out                     empty
Log files:  Total size                     0.41 MB


Cannot list deployed applications.
OMERO data dir:'/data/mongodb-01/OMERO'       Exists? True	Is writable? True
OMERO temp dir:'/home/omero/omero/tmp'        Exists? True	Is writable? True   (Size: 0)

JVM settings: Blitz-${index}                -Xmx7200m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Indexer-${index}              -Xmx4800m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: PixelData-${index}            -Xmx7200m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Repository-${index}           -Xmx4800m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions

It shows the java -version error: ‘NoneType’, but java 1.8 already installed in the server

[omero@cngbdb-d13-11 log]$ java -version
Picked up _JAVA_OPTIONS: -Xmx8G
openjdk version "1.8.0_212"
OpenJDK Runtime Environment (build 1.8.0_212-b04)
OpenJDK 64-Bit Server VM (build 25.212-b04, mixed mode)


Could you please give us the following information:

  • Operating system and version
  • Is this a standard operating system install, or is it customised e.g. by your IT department
  • URL to the instructions you followed to install OMERO.server
  • Whether you have any other applications on the system


As an additional question, is this is a new server installation or a server upgrade?

In the former case, since your PSQL version is 9.4.23, your issue might be related to FYI: Not possible to create new OMERO instance with latest PostgreSQL versions and you might need to downgrade PSQL to the previous patch release.

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