OMERO server 5.6 install difficulties, ubuntu 18.04

I’m running into a couple headscratches on the 5.6 install with ubuntu 18.04. I mostly followed the instructions here, though wasn’t having luck getting the right versions of icegridnode and icegridadmin to show up in omero admin diagnostics so I built and installed ice from source.

The icegridnode server is not running - should the omero server take care of this on start-up or does it need to be addressed first?

$ omero admin diagnostics

================================================================================
OMERO Diagnostics (admin) 5.6.1
================================================================================
        
Commands:   java -version                  11.0.6    (/usr/bin/java)
Commands:   python -V                      3.6.9     (/home/omero/miniconda3/bin/python)
Commands:   icegridnode --version          3.6.5     (/opt/Ice-3.6.5/bin/icegridnode)
Commands:   icegridadmin --version         3.6.5     (/opt/Ice-3.6.5/bin/icegridadmin)
Commands:   psql --version                 11.7      (/usr/bin/psql)
Commands:   openssl version                1.1.1     (/home/omero/miniconda3/bin/openssl -- 2 others)

Server:     icegridnode                    not started

Log dir:    /home/omero/server/OMERO.server/var/log 
No logs available

Environment:OMERO_HOME=(unset)             
Environment:OMERODIR=/home/omero/server/OMERO.server 
Environment:OMERO_NODE=(unset)             
Environment:OMERO_MASTER=(unset)           
Environment:OMERO_USERDIR=(unset)          
Environment:OMERO_TMPDIR=(unset)           
Environment:PATH=/home/omero/miniconda3/bin:/home/omero/miniconda3/bin:/opt/Ice-3.6.5/bin:/home/omero/miniconda3/bin:/home/omero/miniconda3/bin:/home/omero/miniconda3/condabin:/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=/opt/Ice-3.6.5        
Environment:LD_LIBRARY_PATH=/opt/Ice-3.6.5/lib64:/opt/Ice-3.6.5/lib: 
Environment:DYLD_LIBRARY_PATH=(unset)      

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

I have omero-py version 5.6.1 installed, but it is looking for the deprecated omero.properties file which doesn’t ship with OMERO.server 5.6

$ omero admin start
Traceback (most recent call last):
  File "/home/omero/miniconda3/bin/omero", line 118, in <module>
    rv = omero.cli.argv()
  File "/home/omero/miniconda3/lib/python3.6/site-packages/omero/cli.py", line 1754, in argv
    cli.invoke(args[1:])
  File "/home/omero/miniconda3/lib/python3.6/site-packages/omero/cli.py", line 1187, in invoke
    stop = self.onecmd(line, previous_args)
  File "/home/omero/miniconda3/lib/python3.6/site-packages/omero/cli.py", line 1264, in onecmd
    self.execute(line, previous_args)
  File "/home/omero/miniconda3/lib/python3.6/site-packages/omero/cli.py", line 1346, in execute
    args.func(args)
  File "/home/omero/miniconda3/lib/python3.6/site-packages/omero/plugins/prefs.py", line 79, in open_and_close_config
    return func(*args, **kwargs)
  File "/home/omero/miniconda3/lib/python3.6/site-packages/omero/plugins/admin.py", line 810, in start
    self.startasync(args, config)
  File "/home/omero/miniconda3/lib/python3.6/site-packages/omero/plugins/prefs.py", line 79, in open_and_close_config
    return func(*args, **kwargs)
  File "/home/omero/miniconda3/lib/python3.6/site-packages/omero/plugins/admin.py", line 765, in startasync
    self.rewrite(args, config, force=True)
  File "/home/omero/miniconda3/lib/python3.6/site-packages/omero/plugins/prefs.py", line 79, in open_and_close_config
    return func(*args, **kwargs)
  File "/home/omero/miniconda3/lib/python3.6/site-packages/omero/plugins/admin.py", line 1112, in rewrite
    config_props = self._get_omero_properties()
  File "/home/omero/miniconda3/lib/python3.6/site-packages/omero/plugins/admin.py", line 1076, in _get_omero_properties
    (p.key, p.val) for p in pp.parse_file(omero_props_file))
  File "/home/omero/miniconda3/lib/python3.6/site-packages/omero/install/config_parser.py", line 247, in parse_file
    self.parse_lines(fileinput.input(argv))
  File "/home/omero/miniconda3/lib/python3.6/site-packages/omero/install/config_parser.py", line 254, in parse_lines
    for line in lines:
  File "/home/omero/miniconda3/lib/python3.6/fileinput.py", line 250, in __next__
    line = self._readline()
  File "/home/omero/miniconda3/lib/python3.6/fileinput.py", line 362, in _readline
    self._file = open(self._filename, self._mode)
FileNotFoundError: [Errno 2] No such file or directory: path('/home/omero/server/OMERO.server/etc/omero.properties')

Though the grid/config.xml exists and seems accessible.

$ omero config get
omero.data.dir=/omero-data
omero.db.name=omero_database
omero.db.pass=********
omero.db.user=omero
omero.glacier2.IceSSL.Ciphers=HIGH:ADH:@SECLEVEL=0

Is there a config option I am missing? Anything I should try before I start over from the top? Thanks in advance for your time.

OMERO should start the ice components. It sounds like something’s gone wrong with your OMERO.server installation though. Can you show us the output of

ls /home/omero/server/OMERO.server/
ls -R /home/omero/server/OMERO.server/etc
ls -R /home/omero/server/OMERO.server/var

Thanks for the quick reply! Output below

$ ls /home/omero/server/OMERO.server/
db.sql  etc  var
$ ls -R /home/omero/server/OMERO.server/etc
/home/omero/server/OMERO.server/etc:
grid

/home/omero/server/OMERO.server/etc/grid:
config.xml
$ ls -R /home/omero/server/OMERO.server/var
/home/omero/server/OMERO.server/var:

Re-symlinked the OMERO.server-* folder to OMERO.server, redid the configurations, and all set. Thank you for your help, @manics!

Great, thank you for letting us know how it went.