[ome-users] Upgrade problem

Josh Moore josh at glencoesoftware.com
Wed Sep 17 10:20:46 BST 2014 

On Sep 16, 2014, at 9:10 PM, Kotecki, Jason wrote:

> I just performed the following procedure still with no luck.

Hi Jason,

Sorry about the continued troubles.

> ......
> 
> This instance was upgraded from a version 4.x to version 5.0.2. Would that make a difference?

Possibly, but there should still be some indication of what's going wrong. I assume there's still no log file under var\log\Blitz-0.log?

If there's not, then the only things I can think to check are:

1) are any processes currently running?

Could you send us a process listing? Either using procexp from Sysinternals ( http://technet.microsoft.com/en-us/sysinternals/bb896653 ) or minimally with "tasklist /v". You can copy the output to the clipboard via "tasklist /v | clip".


2) what is output if you try running the Java command manually? Something like:

C:\windows\system32\java.exe -Xmx2560m -XX:MaxPermSize=256m -Djava.awt.headless=true -Dlogback.configurationFile=c:\\OMERO.server\\etc\\logback.xml -Domero.logfile=c:\\OMERO.server\\var\\log\\${omero.name}.log -Domero.logbase=/OMERO/ManagedRepository/ -Domero.name=Blitz-0 -jar c:\\OMERO.server\\lib\\server\\blitz.jar --Ice.Config=c:\OMERO.server\var\master/servers/Blitz-0/config/config

Cheers,
~Josh.


> 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>

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