[ome-users] Upgrade problem
Kotecki, Jason
Jason.Kotecki at vai.org
Tue Sep 16 20:10:28 BST 2014
I just performed the following procedure still with no luck.
1. Ran 'omero admin stop'
2. Ran 'omero web iis --remove'
3. Renamed the 'Omero.server' folder to 'Omero.Server_502'
4. Unzipped a newly downloaded v5.0.4 to 'C:\Omero.server'
5. Ran 'iisreset'
6. Rebooted the server
7. Ran 'omero web iis'
8. Ran 'iisreset'
9. Ran the individual omero config commands.
10. Ran 'omero admin start'
The result is the same...
C:\OMERO.server\bin>omero admin start
No descriptor given. Using etc\grid\windefault.xml
Installing OMERO.master Windows service.
Successfully installed OMERO.master Windows service.
Starting OMERO.master Windows service.
Waiting on startup. Use CTRL-C to exit
.............................
Failed to startup some components after 300 seconds
Calling "stop" on remaining components
OMERO.master service deleted.
Waiting on shutdown. Use CTRL-C to exit
......
This instance was upgraded from a version 4.x to version 5.0.2. Would that make a difference?
Best regards,
Jason Kotecki
-----Original Message-----
From: Simon Li [mailto:s.p.li at dundee.ac.uk]
Sent: Monday, September 15, 2014 12:31 PM
To: Kotecki, Jason; Josh Moore
Cc: ome-users at lists.openmicroscopy.org.uk
Subject: Re: [ome-users] Upgrade problem
Hi Jason
Have you managed to get any further with this? An upgrade from 5.0.2 to
5.0.4 hasn¹t shown any obvious problems here on Windows. If not, could you run
> sc query state= all type= service
At a command prompt and see if OMERO.master is listed (I wouldn¹t expect it to be if Blitz failed to start, if it is post the relevant output).
Then perhaps try a reboot and a fresh install: rename your existing 5.0.4 server directory, unzip a fresh server, then run bin\omero config set Š individually for each config line instead of copying an existing config.xml file.
Cheers
Simon
On 11/09/2014 20:48, "Kotecki, Jason" <Jason.Kotecki at vai.org> wrote:
>Sorry. Here is the correct diags file.
>
>-Jason
>
>-----Original Message-----
>From: Josh Moore [mailto:josh at glencoesoftware.com]
>Sent: Thursday, September 11, 2014 3:44 PM
>To: Kotecki, Jason
>Cc: Kenneth Gillen; ome-users at lists.openmicroscopy.org.uk
>Subject: Re: [ome-users] Upgrade problem
>
>
>On Sep 11, 2014, at 9:39 PM, Kotecki, Jason wrote:
>
>> Here you go. Thanks for your help.
>
>It's interesting that Blitz is now running:
>
>Server: Blitz-0 active (pid = 2416, enabled)
>
>
>but there's still no log file:
>
>Log files: Blitz-0.log n/a
>
>
>Is the service bouncing? (i.e. the pid changing frequently)
>
>~J.
>
>
>> -Jason
>>
>> -----Original Message-----
>> From: Josh Moore [mailto:josh at glencoesoftware.com]
>> Sent: Thursday, September 11, 2014 3:37 PM
>> To: Kotecki, Jason
>> Cc: Kenneth Gillen; ome-users at lists.openmicroscopy.org.uk
>> Subject: Re: [ome-users] Upgrade problem
>>
>> And one last data point for the evening with the hopes that I'll be
>> more creative in the morning: could you send the current output of
>> bin\omero admin diagnostics
>>
>> Thanks,
>> ~Josh.
>>
>> On Sep 11, 2014, at 9:31 PM, Kotecki, Jason wrote:
>>
>>> The only errors in the event log are related to the 'ISAPI Filter or
>>>Extension'.
>>>
>>> -Jason
>>>
>>> -----Original Message-----
>>> From: Josh Moore [mailto:josh at glencoesoftware.com]
>>> Sent: Thursday, September 11, 2014 3:09 PM
>>> To: Kotecki, Jason
>>> Cc: Kenneth Gillen; ome-users at lists.openmicroscopy.org.uk
>>> Subject: Re: [ome-users] Upgrade problem
>>>
>>>
>>> On Sep 11, 2014, at 8:40 PM, Kotecki, Jason wrote:
>>>
>>>> I followed your instructions and had the same result. I attached
>>>>the two XML files.
>>>>
>>>> -Jason
>>>
>>> Hmmm....both of the files are well-formed. Is there a new event in
>>>the EventViewer of the form:
>>>
>>>>>> failed to deploy application
>>>>>>`C:\OMERO.server\etc\grid\windefault.xml':
>>>>>> DescriptorParser.cpp:781: IceXML::ParserException error in
>>>>>><C:/OMERO.server/etc/grid/generated.xml> descriptor, line 1,
>>>>>>column
>>>>>>161:
>>>>>> duplicate property set `Blitz'
>>>
>>>
>>> since I certainly only see <properties id="Blitz"> once in your
>>>generated.xml now.
>>>
>>> Thanks for the sleuthing,
>>> ~Josh.
>>>
>>>
>>>> -----Original Message-----
>>>> From: Josh Moore [mailto:josh at glencoesoftware.com]
>>>> Sent: Thursday, September 11, 2014 2:21 PM
>>>> To: Kotecki, Jason
>>>> Cc: Kenneth Gillen; ome-users at lists.openmicroscopy.org.uk
>>>> Subject: Re: [ome-users] Upgrade problem
>>>>
>>>>
>>>> On Sep 11, 2014, at 8:03 PM, Kotecki, Jason wrote:
>>>>
>>>>> Josh, I deleted the generated.xml and tried starting Omero.
>>>>>Unfortunately the result is the same.
>>>>
>>>> And this is with the config.xml copied from your earlier
>>>>installation? If so, could you try:
>>>>
>>>> * (working install) bin\omero config get > config.properties
>>>> * (broken install) delete both config.xml and generated.xml
>>>> * (broken install) bin\omero config load config.properties
>>>> * (broken install) bin\omero admin start
>>>>
>>>> I'm wondering if something has happened with the line-endings which
>>>>is causing the XML generation to fail. (You could also send the two
>>>>XML files for investigation if there are no sensitive passwords in
>>>>the them).
>>>>
>>>> Cheers,
>>>> ~Josh.
>>>>
>>>>> -Jason
>>>>>
>>>>> -----Original Message-----
>>>>> From: Josh Moore [mailto:josh at glencoesoftware.com]
>>>>> Sent: Thursday, September 11, 2014 10:55 AM
>>>>> To: Kotecki, Jason
>>>>> Cc: Kenneth Gillen; ome-users at lists.openmicroscopy.org.uk
>>>>> Subject: Re: [ome-users] Upgrade problem
>>>>>
>>>>>
>>>>> On Sep 11, 2014, at 4:52 PM, Kotecki, Jason wrote:
>>>>>
>>>>>> Josh, when I run in foreground mode this is what I see:
>>>>>>
>>>>>> C:\OMERO.server\bin>omero admin start --foreground No descriptor
>>>>>> given. Using etc\grid\windefault.xml
>>>>>
>>>>> Which makes sense. No errors, so that's a start.
>>>>>
>>>>>
>>>>>> I just checked the event viewer and I do see a warning from
>>>>>>'OMERO.master':
>>>>>>
>>>>>> The description for Event ID 0 from source OMERO.master cannot be
>>>>>>found. Either the component that raises this event is not
>>>>>>installed on your local computer or the installation is corrupted.
>>>>>>You can install or repair the component on the local computer.
>>>>>>
>>>>>> If the event originated on another computer, the display
>>>>>>information had to be saved with the event.
>>>>>>
>>>>>> The following information was included with the event:
>>>>>>
>>>>>> failed to deploy application
>>>>>>`C:\OMERO.server\etc\grid\windefault.xml':
>>>>>> DescriptorParser.cpp:781: IceXML::ParserException error in
>>>>>><C:/OMERO.server/etc/grid/generated.xml> descriptor, line 1,
>>>>>>column
>>>>>>161:
>>>>>> duplicate property set `Blitz'
>>>>>
>>>>> Ah, so this is useful. It does seem like your generated.xml is
>>>>>corrupt. Can you try deleting it and retrying?
>>>>>
>>>>>
>>>>>> There is also an error from 'ISAPI Filter or Extension':
>>>>>> The description for Event ID 4097 from source ISAPI Filter or
>>>>>>Extension cannot be found. Either the component that raises this
>>>>>>event is not installed on your local computer or the installation
>>>>>>is corrupted. You can install or repair the component on the local
>>>>>>computer.
>>>>>>
>>>>>> If the event originated on another computer, the display
>>>>>>information had to be saved with the event.
>>>>>>
>>>>>> The following information was included with the event:
>>>>>>
>>>>>> Failed to import callback module 'omero_web_iis'
>>>>>> Access is denied.
>>>>>
>>>>> Hmmm.... this is not related, but if it persists, we'll need to
>>>>>addresss it as well. But first let's get Blitz running.
>>>>>
>>>>> Thanks for your patience,
>>>>> ~Josh
>>>>>
>>>>>
>>>>>> Thanks,
>>>>>> Jason Kotecki
>>>>>>
>>>>>> -----Original Message-----
>>>>>> From: Josh Moore [mailto:josh at glencoesoftware.com]
>>>>>> Sent: Thursday, September 11, 2014 10:35 AM
>>>>>> To: Kotecki, Jason
>>>>>> Cc: Kenneth Gillen; ome-users at lists.openmicroscopy.org.uk
>>>>>> Subject: Re: [ome-users] Upgrade problem
>>>>>>
>>>>>> Hi Jason,
>>>>>>
>>>>>> On Sep 11, 2014, at 3:56 PM, Kotecki, Jason wrote:
>>>>>>
>>>>>>> Thanks for your help. I have verified the permissions and that
>>>>>>>is not the issue. I downloaded version 5.0.3 and I am
>>>>>>>experiencing the same problem as 5.0.4. The Blitz.log file is not
>>>>>>>created. Did something change from version 5.0.2 that the
>>>>>>>services start differently?
>>>>>>
>>>>>> Not particularly. As you noticed, though, there is a new file
>>>>>>(generated.xml) which allows us to automatically set JVM
>>>>>>properties from etc/grid/templates.xml. Try bin/omero admin jvmcfg
>>>>>>for the values that the server will use.
>>>>>>
>>>>>>
>>>>>>> I noticed that there is a new xml file in the versions after
>>>>>>>5.0.2, /etc/grid/generated.xml. This file has a line related to
>>>>>>>blitz with the word 'REPLACEME'. Is this something I need to change?
>>>>>>>
>>>>>>> <property name="REPLACEMENT:blitz" value="REPLACEME" />
>>>>>>
>>>>>> You shouldn't need to perform any manual replacement.
>>>>>>
>>>>>> Coming late to this thread a couple of questions:
>>>>>> * Have you checked the Windows EventViewer for any errors?
>>>>>> * Did bin\omero admin start --foreground show any errors?
>>>>>>
>>>>>> Cheers,
>>>>>> ~Josh
>>>>>>
>>>>>>
>>>>>>> Thanks,
>>>>>>> Jason
>>>>>>>
>>>>>>> From: Kenneth Gillen [mailto:k.h.gillen at dundee.ac.uk]
>>>>>>> Sent: Wednesday, September 10, 2014 10:19 AM
>>>>>>> To: Kotecki, Jason; ome-users at lists.openmicroscopy.org.uk
>>>>>>> Subject: Re: [ome-users] Upgrade problem
>>>>>>>
>>>>>>> The only thing I've had trouble with, using that exact workflow,
>>>>>>>is not adding the OMERO service user's permissions to access the
>>>>>>>new folder c:\OMERO.server after creating it for the latest OMERO
>>>>>>>upgrade - worth checking that.
>>>>>>>
>>>>>>> Best,
>>>>>>>
>>>>>>> Kenny
>>>>>>>
>>>>>>> --
>>>>>>>
>>>>>>> Kenneth Gillen
>>>>>>> OME System Administrator
>>>>>>>
>>>>>>> Wellcome Trust Centre for Gene Regulation & Expression College
>>>>>>> of Life Sciences MSI/WTB/JBC Complex University of Dundee Dow
>>>>>>> Street Dundee
>>>>>>> DD1 5EH United Kingdom
>>>>>>>
>>>>>>> Tel: +44 (0) 1382 386364
>>>>>>> Skype: kennethgillen
>>>>>>>
>>>>>>> http://scanmail.trustwave.com/?c=129&d=47SR1FVGblQi-14COp4zgQSJD
>>>>>>> N
>>>>>>> -
>>>>>>> X
>>>>>>> I
>>>>>>> N
>>>>>>> 0
>>>>>>>
>>>>>>>c1u_sd4uoxA&u=http%3a%2f%2fwww%2etwitter%2ecom%2fopenmicroscopy<h
>>>>>>>ttp
>>>>>>>:
>>>>>>> /
>>>>>>>
>>>>>>>/scanmail.trustwave.com/?c=129&d=47SR1FVGblQi-14COp4zgQSJDN-XIN0c
>>>>>>> 1 u _ s d
>>>>>>> 4uoxA&u=http%3a%2f%2fwww%2etwitter%2ecom%2fopenmicroscopy>
>>>>>>>
>>>>>>> From: <Kotecki>, Jason
>>>>>>> <Jason.Kotecki at vai.org<mailto:Jason.Kotecki at vai.org>>
>>>>>>> Date: Wednesday, 10 September 2014 15:11
>>>>>>> To:
>>>>>>> "ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.op
>>>>>>> e
>>>>>>> n
>>>>>>> m
>>>>>>> i
>>>>>>> c
>>>>>>> r
>>>>>>>
>>>>>>>http://scanmail.trustwave.com/?c=129&d=hfuR1JjEbat4yyYn1cx0CLO3ma
>>>>>>>O1m JlF2EMSmpRSkw&u=http%3a%2f%2foscopy%2eorg%2euk>"
>>>>>>>
>>>>>>><ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.ope
>>>>>>> n
>>>>>>> m
>>>>>>> i
>>>>>>> c
>>>>>>> r
>>>>>>>
>>>>>>>http://scanmail.trustwave.com/?c=129&d=0beR1HQ5DR6Yi55RjWru_1xBac
>>>>>>> D
>>>>>>> 3 Z M -nEopOe2A80A&u=http%3a%2f%2foscopy%2eorg%2euk>>
>>>>>>> Subject: [ome-users] Upgrade problem
>>>>>>>
>>>>>>> Hello, I recently attempted the upgrade from 5.0.2 to 5.0.4. I'm
>>>>>>>running on a Windows server using IIS. The process I did was:
>>>>>>>
>>>>>>> 1. Backup the database
>>>>>>>
>>>>>>> 2. Ran 'omero admin stop'
>>>>>>>
>>>>>>> 3. Ran 'omero web iis -remove'
>>>>>>>
>>>>>>> 4. Renamed the 'Omero.server' folder to 'Omero.server.OLD'
>>>>>>>
>>>>>>> 5. Extracted the 'OMERO.server-5.0.4-ice34-b43.zip' to
>>>>>>>'Omero.server.
>>>>>>>
>>>>>>> 6. Copied the '/etc/grid/config.xml' file from my old folder
>>>>>>>to the new folder.
>>>>>>>
>>>>>>> 7. Ran 'omero web iis'
>>>>>>>
>>>>>>> 8. Ran 'omero admin start'.
>>>>>>>
>>>>>>> Here is the output of that start command:
>>>>>>>
>>>>>>> C:\OMERO.server\bin>omero admin start No descriptor given. Using
>>>>>>>etc\grid\windefault.xml Installing OMERO.master Windows service.
>>>>>>> Successfully installed OMERO.master Windows service.
>>>>>>> Starting OMERO.master Windows service.
>>>>>>> Waiting on startup. Use CTRL-C to exit
>>>>>>>.............................
>>>>>>> Failed to startup some components after 300 seconds Calling "stop"
>>>>>>> on remaining components OMERO.master service deleted.
>>>>>>> Waiting on shutdown. Use CTRL-C to exit C:\OMERO.server\bin>
>>>>>>>
>>>>>>> I also attached the results of the 'omero admin diagnostics'
>>>>>>>command.
>>>>>>>
>>>>>>> Thanks,
>>>>>>> Jason Kotecki
>>>> <generated.xml><config.xml>
>> <omero_diags.txt>
The University of Dundee is a registered Scottish Charity, No: SC015096
More information about the ome-users
mailing list