[ome-users] Upgrade problem

Anatole Chessel anatole.chessel at gurdon.cam.ac.uk
Thu Sep 18 10:55:25 BST 2014 

Actually, I just realised that a bunch of errors/informations are logged 
in the windows event viewer, which may help diagnose things:
4 information events, from OMERO.master:
-'Berkeley DB: DbEnv "Registry": Unacceptable log file 
C:\Users\omero\Desktop\OMERO.server-5.0.4-ice34-b43\var\registry\log.0000000001: 
unsupported log version 19'
-'Berkeley DB: DbEnv "Registry": Invalid log file: log.0000000001: 
Invalid argument'
-'Berkeley DB: DbEnv "Registry": PANIC: Invalid argument'
-'Berkeley DB: DbEnv "Registry": process-private: unable to find 
environment'

2 errors events, the first from OMERO.master, the second from Service 
Control Manager:
-'exception occurred while initializing a communicator:
SharedDbEnv.cpp:619: Freeze::DatabaseException:
DbEnv::open: DB_RUNRECOVERY: Fatal error, run database recovery'
-'The OMERO.master service terminated with service-specific error 
Incorrect function..'

Hope that helps,
A.

On 17/09/2014 13:57, Anatole Chessel wrote:
> 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
>
>
> _______________________________________________
> 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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