[ome-users] Upgrade problem

Anatole Chessel anatole.chessel at gurdon.cam.ac.uk
Wed Sep 17 13:57:36 BST 2014 

Hi all,

I seem to be having the exact same problem. I am trying to upgrade from 
4.4 to 5.0.4 on a windows server 2008R2; after trying without success 
the OME compiled ice3.5/python2.7 64bit (full thread: 
http://www.openmicroscopy.org/community/viewtopic.php?f=5&t=7629&start=10 in 
short omero eventually worked but omero.web did not), I tried 
ice3.4/python2.6 32bits with the same issues as Jason: 'Failed to 
startup some components after 300 seconds' and no logs, and launching 
manually gives a logfile with the same error he just reported...

Many thanks,
A.


On 17/09/2014 13:36, Kotecki, Jason wrote:
> Josh, attached is the task list. Also, I ran the command for blitz manually and that actually created a log file.
>
> Thanks,
> Jason
>
> -----Original Message-----
> From: Josh Moore [mailto:josh at glencoesoftware.com]
> Sent: Wednesday, September 17, 2014 5:21 AM
> To: Kotecki, Jason
> Cc: Simon Li; ome-users at lists.openmicroscopy.org.uk
> Subject: Re: [ome-users] Upgrade problem
>
>
> 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://scanmail.trustwave.com/?c=129&d=8NKZ1L9jDCHt-Aic-p4xTcOqd5mDInJOXMXxx-2lJA&u=http%3a%2f%2ftechnet%2emicrosoft%2ecom%2fen-us%2fsysinternals%2fbb896653 ) 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 S( 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-14COp4zgQSJ
>>>>>>>>> D
>>>>>>>>> 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-XIN
>>>>>>>>> 0c
>>>>>>>>> 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.o
>>>>>>>>> p
>>>>>>>>> e
>>>>>>>>> n
>>>>>>>>> m
>>>>>>>>> i
>>>>>>>>> c
>>>>>>>>> r
>>>>>>>>>
>>>>>>>>> http://scanmail.trustwave.com/?c=129&d=hfuR1JjEbat4yyYn1cx0CLO3
>>>>>>>>> ma O1m JlF2EMSmpRSkw&u=http%3a%2f%2foscopy%2eorg%2euk>"
>>>>>>>>>
>>>>>>>>> <ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.o
>>>>>>>>> pe
>>>>>>>>> n
>>>>>>>>> m
>>>>>>>>> i
>>>>>>>>> c
>>>>>>>>> r
>>>>>>>>>
>>>>>>>>> http://scanmail.trustwave.com/?c=129&d=0beR1HQ5DR6Yi55RjWru_1xB
>>>>>>>>> ac
>>>>>>>>> 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>
>>>>
>>>>
>>>> _______________________________________________
>>>> ome-users mailing list
>>>> ome-users at lists.openmicroscopy.org.uk
>>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users

-- 
Anatole Chessel, PhD
Research associate
University of Cambridge
Tennis Court Road, Cambridge CB2 1PD
tel: +44 (0)1223 334065

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