[ome-users] Upgrade problem
Josh Moore
josh at glencoesoftware.com
Thu Sep 11 20:44:12 BST 2014
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-14COp4zgQSJDN-
>>>>>> X
>>>>>> I
>>>>>> N
>>>>>> 0
>>>>>> c1u_sd4uoxA&u=http%3a%2f%2fwww%2etwitter%2ecom%2fopenmicroscopy<http:
>>>>>> /
>>>>>> /scanmail.trustwave.com/?c=129&d=47SR1FVGblQi-14COp4zgQSJDN-XIN0c1
>>>>>> 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.open
>>>>>> m
>>>>>> i
>>>>>> c
>>>>>> r
>>>>>> http://scanmail.trustwave.com/?c=129&d=vvmR1ANrj2OKFBKAXoTtg1EiRF_Pp8kUxBIbMsbOGw&u=http%3a%2f%2foscopy%2eorg%2euk>"
>>>>>> <ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.open
>>>>>> m
>>>>>> i
>>>>>> c
>>>>>> r
>>>>>> http://scanmail.trustwave.com/?c=129&d=0beR1HQ5DR6Yi55RjWru_1xBacD
>>>>>> 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>
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