Open Microscopy Environment

Hi everyone,

I'm new to the whole OMERO and Open Microscopy world and I'm looking for some assistance in regard to setting up a fresh install of OMERO on a Ubuntu 16.04 server.

Here are the server specs:
OS: Ubuntu server 16.04
Memory: 4GB
Hard Disk: 1TB

I followed the following instructions exactly as directed:

https://docs.openmicroscopy.org/omero/5 ... ice36.html

Here are the versions of the software that I have successfully installed with no errors:
================================================================================
OMERO Diagnostics (admin) 5.4.10-ice36-b105
================================================================================

Commands: java -version 1.8.0 (/usr/bin/java)
Commands: python -V 2.7.12 (/usr/bin/python)
Commands: icegridnode --version 3.6.4 (/usr/bin/icegridnode)
Commands: icegridadmin --version 3.6.4 (/usr/bin/icegridadmin)
Commands: psql --version 9.6.12 (/usr/bin/psql)

Here is the error that I get when I try to start OMERO:
omero@OMERO:~$ OMERO.server/bin/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
......omero@OMERO:~$

Any assistance on the startup of OMERO would be appreciated. I have attached the OMERO logs for reference, I attempted to decipher them but I'm not familiar with the log syntax or what to look for. Thanks.

Hello, welcome to OMERO! I'm afraid I can't see where you attached the logs? You can also zip them up and submit them to http://qa.openmicroscopy.org.uk/qa/upload/ if that's easier; Blitz-0.log should be of especial interest.

What does "bin/omero config get" give? All that looks correct?

Cheers,
Mark

Not sure what happened, I have zipped them up and attached them for your reference.

Here are the results of the config file:

omero@OMERO:~$ OMERO.server/bin/omero config get
omero.data.dir=/OMERO
omero.db_name=omero_database
omero.db_pass=********
omero.db_user=&OMERO_DB_USER

I confirmed the directory, database name, and db username and password.

Thanks for the help.

Two things that stand out immediately:

• Your PostgreSQL database user is indeed named "&OMERO_DB_USER"?
• The configuration property keys shouldn't have underscores, e.g., you need omero.db.user rather than omero.db_user.

Your Blitz-0.log confirms that the problem is in trying to authenticate to the database.

I hope this helps!

Cheers,
Mark

Thanks for the help, that was my issue. I corrected the omero environment variables and the service started up! I ran diagnostics and I was wondering if you can tell me if the errors in the log files are normal for a new install or if more investigation needs to happen.

omero@OMERO:~$ OMERO.server/bin/omero admin diagnostics

================================================================================
OMERO Diagnostics (admin) 5.4.10-ice36-b105
================================================================================

Commands: java -version 1.8.0 (/usr/bin/java)
Commands: python -V 2.7.12 (/usr/bin/python)
Commands: icegridnode --version 3.6.4 (/usr/bin/icegridnode)
Commands: icegridadmin --version 3.6.4 (/usr/bin/icegridadmin)
Commands: psql --version 9.6.12 (/usr/bin/psql)

Server: icegridnode running
Server: Blitz-0 active (pid = 4347, enabled)
Server: DropBox active (pid = 4359, enabled)
Server: FileServer active (pid = 4365, enabled)
Server: Indexer-0 active (pid = 4372, enabled)
Server: MonitorServer active (pid = 4361, enabled)
Server: OMERO.Glacier2 active (pid = 4368, enabled)
Server: OMERO.IceStorm active (pid = 4370, enabled)
Server: PixelData-0 active (pid = 4364, enabled)
Server: Processor-0 active (pid = 4375, enabled)
Server: Tables-0 active (pid = 4384, enabled)
Server: TestDropBox inactive (enabled)

Log dir: /home/omero/OMERO.server/var/log exists
Log files: 192.168.5.135 401.0 KB errors=22 warnings=33
Log files: @192.168.5.135 401.0 KB errors=22 warnings=33
Log files: Blitz-0.log 1.0 MB errors=28 warnings=42
Log files: DropBox.log 22.0 KB errors=28 warnings=14
Log files: FileServer.log 4.0 KB
Log files: Indexer-0.log 645.0 KB errors=28 warnings=43
Log files: MonitorServer.log 5.0 KB
Log files: PixelData-0.log 645.0 KB errors=28 warnings=42
Log files: Processor-0.log 654.0 KB errors=173 warnings=346
Log files: Tables-0.log 657.0 KB errors=173 warnings=346
Log files: TestDropBox.log n/a
Log files: master.err 8.0 KB errors=14 warnings=15
Log files: master.out 0.0 KB
Log files: Total size 4.63 MB


Environment:OMERO_HOME=(unset)
Environment:OMERO_NODE=(unset)
Environment:OMERO_MASTER=(unset)
Environment:OMERO_USERDIR=(unset)
Environment:OMERO_TMPDIR=(unset)
Environment:PATH=/home/omero/bin:/home/omero/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin
Environment:PYTHONPATH=(unset)
Environment:ICE_HOME=(unset)
Environment:LD_LIBRARY_PATH=(unset)
Environment:DYLD_LIBRARY_PATH=(unset)

OMERO SSL port:4064
OMERO TCP port:4063
OMERO data dir:'/OMERO' Exists? True Is writable? True
OMERO temp dir:'/home/omero/omero/tmp' Exists? True Is writable? True (Size: 31575)

JVM settings: Blitz-${index} -Xmx619m -XX:MaxPermSize=512m -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Indexer-${index} -Xmx413m -XX:MaxPermSize=512m -XX:+IgnoreUnrecognizedVMOptions
JVM settings: PixelData-${index} -Xmx619m -XX:MaxPermSize=512m -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Repository-${index} -Xmx413m -XX:MaxPermSize=512m -XX:+IgnoreUnrecognizedVMOptions
omero@OMERO:~$

Thanks again.

If the same log files could include the earlier database authentication problems then many errors are to be expected. You may want to stop the server, move those log files out of the way completely, restart it then see what happens henceforth. A couple of warnings are usual but not much more than that.

If you can attach some logs that postdate your configuration fix we could take a look if you like, or if you see any puzzling WARN or ERROR lines appearing more recently that you'd like to ask about, feel free to paste the surrounding extract and we'll try to help you interpret them.

It's good you're checking and asking. For our OMERO production servers we have alerting that routinely keeps an eye on the logs for any signs of new trouble.

Cheers,
Mark