Open Microscopy Environment

I'm trying to get omero 4.3.2 server set up on a sles 11 sp1 system and running into problems with versions of Ice. I initially followed the install doc strictly, and installed Ice 3.3.1... all seemed fine until I tried to run"bin/omero config set omero.db.name 'myDatabase'" - It immediately returned an error that the module Icepy could not be found. After some googling, I tried adding a repo for Ice directly from zeroc.com, and used it to upgrade my Ice install to 3.4.2... after this I was able to get the database configured, but bin/omero
admin start now yields :

omerouser@omero:/OMERO/OMERO.server-Beta-4.3.2> bin/omero admin start
No handlers could be found for logger "omero.util.TempFileManager"
IcePy Version is not compatible with ^3[.]3[.].*: 3.4.2

Output of omero admin diagnostics below (apologies for the huge post)

Anyone run into anything similar before? Any tips or info would be appreciated.



omerouser@omero:/OMERO/OMERO.server-Beta-4.3.2> bin/omero admin diagnostics
No handlers could be found for logger "omero.util.TempFileManager"

================================================================================
OMERO Diagnostics 4.3.2-8fc94b85-b2882
================================================================================

Commands: java -version 1.7.0 (/usr/bin/java -- 2 others)
Commands: python -V 2.6 (/usr/bin/python)
Commands: icegridnode --version 3.4.2 (/usr/bin/icegridnode)
Commands: icegridadmin --version 3.4.2 (/usr/bin/icegridadmin)
Commands: psql --version 8.3.9 (/usr/bin/psql)

Server: icegridnode not started

Log dir: /OMERO/OMERO.server-Beta-4.3.2/var/log n/a


Error while parsing logs

Environment:OMERO_HOME=(unset)
Environment:OMERO_NODE=(unset)
Environment:OMERO_MASTER=(unset)
Environment:PATH=/opt/quest/bin:/root/bin:/usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/usr/X11R6/bin:/usr/games:/usr/lib/mit/bin:/usr/lib/mit/sbin:/usr/java/jdk1.7.0/jre/bin:/usr/java/jdk1.7.0/jre/bin:/usr/share/Ice-3.3.1/bin:POSTGRES_HOME/bin:/usr/lib64/python/site-packages/Ice:/usr/java/jdk1.7.0/jre/bin:/usr/java/jdk1.7.0/jre/bin:/usr/share/Ice-3.3.1/bin:POSTGRES_HOME/bin:/usr/lib64/python/site-packages/Ice:/usr/java/jdk1.7.0/jre/bin:/usr/java/jdk1.7.0/jre/bin:/usr/share/Ice-3.4.2/bin:POSTGRES_HOME/bin:/usr/lib64/python/site-packages/Ice
Environment:ICE_HOME=/usr/share/Ice-3.4.2
Environment:LD_LIBRARY_PATH=/usr/share/java:/usr/lib:/usr/share/java:/usr/lib:/usr/share/java:/usr/lib:
Environment:DYLD_LIBRARY_PATH=/usr/share/java:/usr/lib/:/usr/share/java:/usr/lib/:/usr/share/java:/usr/lib/:

OMERO data dir: '/OMERO' Exists? True Is writable? True
OMERO.web status... Traceback (most recent call last):
File "bin/omero", line 123, in <module>
rv = omero.cli.argv()
File "/OMERO/OMERO.server-Beta-4.3.2/lib/python/omero/cli.py", line 1172, in argv
cli.invoke(args[1:])
File "/OMERO/OMERO.server-Beta-4.3.2/lib/python/omero/cli.py", line 722, in invoke
stop = self.onecmd(line, previous_args)
File "/OMERO/OMERO.server-Beta-4.3.2/lib/python/omero/cli.py", line 791, in onecmd
self.execute(line, previous_args)
File "/OMERO/OMERO.server-Beta-4.3.2/lib/python/omero/cli.py", line 871, in execute
args.func(args)
File "/OMERO/OMERO.server-Beta-4.3.2/lib/python/omero/plugins/prefs.py", line 67, in open_and_close_config
return func(*args, **kwargs)
File "/OMERO/OMERO.server-Beta-4.3.2/lib/python/omero/plugins/admin.py", line 780, in diagnostics
WebControl().status(args)
File "/OMERO/OMERO.server-Beta-4.3.2/lib/python/omero/plugins/web.py", line 391, in status
import omeroweb.settings as settings
File "/OMERO/OMERO.server-Beta-4.3.2/lib/python/omeroweb/settings.py", line 34, in <module>
import omero.clients
File "/OMERO/OMERO.server-Beta-4.3.2/lib/python/omero/clients.py", line 13, in <module>
model = __import__('omero.model')
File "/OMERO/OMERO.server-Beta-4.3.2/lib/python/omero/model/__init__.py", line 2, in <module>
map()
File "/OMERO/OMERO.server-Beta-4.3.2/lib/python/omero/util/FactoryMap.py", line 11, in map
import omero.model, omero_model_PermissionsI, omero_model_DetailsI
File "/OMERO/OMERO.server-Beta-4.3.2/lib/python/omero_model_PermissionsI.py", line 11, in <module>
import omero_model_Permissions_ice
File "/OMERO/OMERO.server-Beta-4.3.2/lib/python/omero_model_Permissions_ice.py", line 17, in <module>
import omero_model_IObject_ice
File "/OMERO/OMERO.server-Beta-4.3.2/lib/python/omero_model_IObject_ice.py", line 129, in <module>
('_details', (), _M_omero.model._t_Details),
AttributeError: 'module' object has no attribute '_t_Details'

Quite simply OMERO does not support Ice 3.4.x. You'll need to find a way to get IcePy 3.3.1 installed on SLES 11 SP1. I'd be more specific but I haven't used SUSE since before it was bought by Novell.

Thanks, I've abandoned sles for the time being... I have the server up and running on a centos 5.6 system, and overall the install process has gone much smoother. However, I am now stuck because the webadmin interface as well as the insight client won't take any user/pass combo, all I get is "Error: Connection not available, please check your user name and password". I've confirmed the username/password combo is correct, there is no firewall enabled...

Thanks for the help, diag output:


[omerouser@omero2 OMERO.server-Beta-4.3.2]$ bin/omero admin diagnostics

================================================================================
OMERO Diagnostics 4.3.2-8fc94b85-b2882
================================================================================

Commands: java -version 1.7.0 (/usr/bin/java)
Commands: python -V 2.4.3 (/usr/bin/python)
Commands: icegridnode --version 3.3.1 (/usr/bin/icegridnode)
Commands: icegridadmin --version 3.3.1 (/usr/bin/icegridadmin)
Commands: psql --version 8.3.11 (/usr/bin/psql)

Server: icegridnode running
Server: Blitz-0 active (pid = 25458, enabled)
Server: DropBox inactive (disabled)
Server: FileServer active (pid = 25476, enabled)
Server: Indexer-0 active (pid = 25477, enabled)
Server: MonitorServer inactive (disabled)
Server: OMERO.Glacier2 active (pid = 25492, enabled)
Server: OMERO.IceStorm active (pid = 25491, enabled)
Server: PixelData-0 active (pid = 25528, enabled)
Server: Processor-0 active (pid = 25530, enabled)
Server: Tables-0 inactive (disabled)
Server: TestDropBox inactive (enabled)

Log dir: /OMERO/OMERO.server-Beta-4.3.2/var/log exists

Log files: Blitz-0.log 124.0 KB errors=0 warnings=9
Log files: DropBox.log 1.0 KB errors=1 warnings=0
Log files: FileServer.log 0.0 KB
Log files: Indexer-0.log 49.0 KB
Log files: MonitorServer.log 0.0 KB errors=1 warnings=0
Log files: OMEROweb.log 10.0 KB errors=2 warnings=0
Log files: PixelData-0.log 1.0 KB
Log files: Processor-0.log 0.0 KB
Log files: Tables-0.log n/a
Log files: TestDropBox.log n/a
Log files: master.err 0.0 KB
Log files: master.out 0.0 KB
Log files: Total size 0.19 MB

Parsing Blitz-0.log:[line:106] => Server restarted <=

Environment:OMERO_HOME=(unset)
Environment:OMERO_NODE=(unset)
Environment:OMERO_MASTER=(unset)
Environment:PATH=/usr/kerberos/sbin:/usr/kerberos/bin:/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/root/bin:/usr/java/default/bin
Environment:ICE_HOME=(unset)
Environment:LD_LIBRARY_PATH=(unset)
Environment:DYLD_LIBRARY_PATH=(unset)

OMERO data dir: '/OMERO' Exists? True Is writable? True
OMERO.web status... DEVELOPMENT: You will have to check status by hand!

rb-mdi wrote:However, I am now stuck because the webadmin interface as well as the insight client won't take any user/pass combo, all I get is "Error: Connection not available, please check your user name and password". I've confirmed the username/password combo is correct, there is no firewall enabled...

The diagnostics output looks at least nominally healthy. How did you go about checking the username/password combo? Are you logging in as root? You might want to take a look at "Which password do I use where?" under "Troubleshooting". If that's not the issue, you might try resetting the root password. And if that doesn't work, it'd probably be useful to take a look at some of your server logs like var/log/Blitz-0.log.

Cheers,
~Josh.

Thanks, I'm in now... I likely fat-fingered the omero root password when I initially set up the installation. Thanks for your help

Glad to hear it wasn't something more serious! Cheers, ~Josh.