Problem when installing Omero Server 5.5 (Ubuntu 18.04 Server / Hyper-V)

I’m trying to setup a test OMERO.Server on a Hyper-V Machine running a freshly installed Ubuntu 18.04 Server system, following the described walkthrough.
During the installation no errors are encountered, only when running

systemctl --now disable glacier2router icegridregistry

the response is:

Failed to disable unit: Unit file glacier2router.service does not exist.

When I try to start the server for the first time:

OMERO.server/bin/omero admin start

it fails (see Python Traceback below):

Traceback (most recent call last):
File “OMERO.server/bin/omero”, line 130, in
rv = omero.cli.argv()
File “/home/omero/OMERO.server/lib/python/omero/cli.py”, line 1706, in argv
cli.invoke(args[1:])
File “/home/omero/OMERO.server/lib/python/omero/cli.py”, line 1159, in invoke
stop = self.onecmd(line, previous_args)
File “/home/omero/OMERO.server/lib/python/omero/cli.py”, line 1236, in onecmd
self.execute(line, previous_args)
File “/home/omero/OMERO.server/lib/python/omero/cli.py”, line 1318, in execute
args.func(args)
File “/home/omero/OMERO.server/lib/python/omero/plugins/prefs.py”, line 74, in open_and_close_config
return func(*args, **kwargs)
File “/home/omero/OMERO.server/lib/python/omero/plugins/admin.py”, line 803, in start
self.startasync(args, config)
File “/home/omero/OMERO.server/lib/python/omero/plugins/prefs.py”, line 74, in open_and_close_config
return func(*args, **kwargs)
File “/home/omero/OMERO.server/lib/python/omero/plugins/admin.py”, line 754, in startasync
self.checkice()
File “/home/omero/OMERO.server/lib/python/omero/plugins/admin.py”, line 1651, in checkice
popen = self.ctx.popen([“icegridnode”, “–version”])
File “/home/omero/OMERO.server/lib/python/omero/cli.py”, line 1409, in popen
stdout=stdout, stderr=stderr)
File “/usr/lib/python2.7/subprocess.py”, line 394, in init
errread, errwrite)
File “/usr/lib/python2.7/subprocess.py”, line 1047, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory

When running the diganostics tools, it produces the following output:

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

================================================================================
OMERO Diagnostics (admin) 5.5.0-ice36-b121

Commands: java -version 1.8.0 (/usr/bin/java)
Commands: python -V 2.7.15 (/usr/bin/python)
Commands: icegridnode --version not found
Commands: icegridadmin --version not found
Commands: psql --version 10.8 (/usr/bin/psql)

No icegridadmin available: Cannot check server list

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

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:/snap/bin
Environment:PYTHONPATH=(unset)
Environment:ICE_HOME=(unset)
Environment:LD_LIBRARY_PATH=(unset)
Environment:DYLD_LIBRARY_PATH=(unset)

Traceback (most recent call last):
File “OMERO.server/bin/omero”, line 130, in
rv = omero.cli.argv()
File “/home/omero/OMERO.server/lib/python/omero/cli.py”, line 1706, in argv
cli.invoke(args[1:])
File “/home/omero/OMERO.server/lib/python/omero/cli.py”, line 1159, in invoke
stop = self.onecmd(line, previous_args)
File “/home/omero/OMERO.server/lib/python/omero/cli.py”, line 1236, in onecmd
self.execute(line, previous_args)
File “/home/omero/OMERO.server/lib/python/omero/cli.py”, line 1318, in execute
args.func(args)
File “/home/omero/OMERO.server/lib/python/omero/install/windows_warning.py”, line 26, in wrapper
return func(self, *args, **kwargs)
File “/home/omero/OMERO.server/lib/python/omero/plugins/prefs.py”, line 74, in open_and_close_config
return func(*args, **kwargs)
File “/home/omero/OMERO.server/lib/python/omero/plugins/admin.py”, line 1422, in diagnostics
p = self.ctx.popen(self._cmd("-e", “application list”)) # popen
File “/home/omero/OMERO.server/lib/python/omero/cli.py”, line 1409, in popen
stdout=stdout, stderr=stderr)
File “/usr/lib/python2.7/subprocess.py”, line 394, in init
errread, errwrite)
File “/usr/lib/python2.7/subprocess.py”, line 1047, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory

I’m worried, that icegridnode and icegridadmin are not defined.
Any thoughts on the issue would be appreciated.
Best
Martin

Hi Martin

It looks like ice 3.6 is not available to the relevant users. You will have to make it available see for example https://github.com/ome/omero-install/blob/develop/linux/install_ubuntu1804_nginx.sh#L22
and https://github.com/ome/omero-install/blob/develop/linux/omero-ice36.env

Cheers
Jmarie

1 Like

Hi Jmarie,

many thanks, this solved it. Creating omero-ice36.sh in /etc/profile.d/ with the following content solved the issue:

export ICE_HOME=/opt/Ice-3.6.4
export PATH="$ICE_HOME/bin:$PATH"

Maybe this should be part of the walkthrough (https://docs.openmicroscopy.org/omero/5.5.0/sysadmins/unix/server-ubuntu1804-ice36.html)?

Many thanks for the quick help
Martin

1 Like

Great that the problem is solved.
We will update the walkthrough so it is included for Debian 9 and Ubuntu 18.04 doc

cheers
Jmarie