[ome-users] Upgrade problem

Simon Li s.p.li at dundee.ac.uk
Mon Sep 15 17:30:35 BST 2014 

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-14COp4zgQSJDN
>>>>>>> -
>>>>>>> X
>>>>>>> I
>>>>>>> N
>>>>>>> 0
>>>>>>>
>>>>>>>c1u_sd4uoxA&u=http%3a%2f%2fwww%2etwitter%2ecom%2fopenmicroscopy<http
>>>>>>>:
>>>>>>> /
>>>>>>> /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.ope
>>>>>>> n
>>>>>>> m
>>>>>>> i
>>>>>>> c
>>>>>>> r
>>>>>>>
>>>>>>>http://scanmail.trustwave.com/?c=129&d=hfuR1JjEbat4yyYn1cx0CLO3maO1m
>>>>>>>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>


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