[ome-users] OME.insight not working after upgrade
Douglas Russell
douglas.russell at bioch.ox.ac.uk
Fri Dec 5 14:27:49 GMT 2014
If you are sure the server is running you could also run something like
this on the sever:
netstat -l -n --program
This will display the ports that various processes are running on. You'll
have to sift the results, but on a working server (on port 4064) you will
see something like this among them:
tcp6 0 0 :::4064 :::* LISTEN
27482/glacier2route
If that is there, then you likely have the firewall issue that Kenny
suggested.
Hope that (or your IT) helps.
Douglas
On 5 December 2014 at 11:06, <unai_lorenzo at ehu.es> wrote:
> Hi Douglas,
>
> Unfortunately it failed (I'm sorry, the code is in Spanish...)
>
> telnet 158.227.41.112 4064
> Conectándose a 158.227.41.112...No se puede abrir la conexión al host, en
> puerto 4064: Error en la conexión
>
> As Kenny suggested, I will contact the IT department and see if we can fix
> it.
>
> Kind regards,
> Unai
>
>
> Douglas Russell <douglas.russell at bioch.ox.ac.uk> escribió:
>
>
> Easiest way to tell if you can connect to a port on a server, regardless
>> of
>> protocol:
>>
>> telnet servername port_number
>>
>> e.g. Success:
>>
>> $ telnet omero1.bioch.ox.ac.uk 4064
>> Trying 129.67.75.47...
>> Connected to omero1.bioch.ox.ac.uk.
>> Escape character is '^]'.
>>
>> Fail:
>>
>> $ telnet omero1.bioch.ox.ac.uk 9999
>> Trying 129.67.75.47...
>> telnet: connect to address 129.67.75.47: Connection refused
>> telnet: Unable to connect to remote host
>>
>>
>>
>> On 5 December 2014 at 09:38, Kenneth Gillen (Staff) <
>> k.h.gillen at dundee.ac.uk
>>
>>> wrote:
>>>
>>
>> HI Unai,
>>>
>>> This sounds like the an issue connecting on the OMERO ports.
>>>
>>> I’d check that the Insight connection dialogue has the correct server
>>> ports which correspond to the setup of your server.
>>>
>>> If you can’t access that server from your workstations, then you’ll
>>> probably need to interact with your local network management team to work
>>> out why. Changes are, the changed a policy, and the ports are blocked.
>>>
>>> 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://www.twitter.com/openmicroscopy
>>>
>>>
>>>
>>>
>>>
>>>
>>> On 05/12/2014 09:19, "unai_lorenzo at ehu.es" <unai_lorenzo at ehu.es> wrote:
>>>
>>> >Hi Josh,
>>> >
>>> >I can login using bin\omero login localhost (both as root and as a
>>> >"normal" user).
>>> >I can also ping successfully the server IP address from the client PC.
>>> >
>>> >Many thanks,
>>> >Unai
>>> >
>>> >Josh Moore <josh at glencoesoftware.com> escribió:
>>> >
>>> >> Hi Unai,
>>> >>
>>> >> from the log it most looks like insight cannot reach the server at
>>> all,
>>> >>as
>>> >> if the port were not available. I assume you have access to the server
>>> >>and
>>> >> could attempt trying to login with:
>>> >>
>>> >> bin\omero login localhost
>>> >>
>>> >> Cheers,
>>> >> ~Josh.
>>> >>
>>> >>
>>> >> On Thu, Dec 4, 2014 at 12:11 PM, <unai_lorenzo at ehu.es> wrote:
>>> >>
>>> >>> Hi Kenny,
>>> >>>
>>> >>> I'm currently using OMERO.clients-5.0.6-ice35-b53.win pltaform.
>>> Before
>>> >>> the upgrade I was using OMERO.clients-5.0.5-ice35-b47.win, and this
>>> one
>>> >>> doesn't work after the upgrade either.
>>> >>>
>>> >>> Please find attached the client log file. I hope it helps!
>>> >>>
>>> >>> Best regards,
>>> >>> Unai
>>> >>>
>>> >>>
>>> >>> "Kenneth Gillen (Staff)" <k.h.gillen at dundee.ac.uk> escribió:
>>> >>>
>>> >>> Hi Unai,
>>> >>>>
>>> >>>> Could you please send us your insight client log file, as well as
>>> >>>>letting
>>> >>>> us know which platform client you are using?
>>> >>>>
>>> >>>> See ŒClient logs¹ at
>>> >>>> http://www.openmicroscopy.org/site/support/faq/omero/how-do-
>>> >>>> i-send-log-file
>>> >>>> s
>>> >>>>
>>> >>>> I would doubt that there is anything sensitive in that log file, but
>>> >>>>worth
>>> >>>> a quick scan before sending to the list.
>>> >>>>
>>> >>>> Many thanks,
>>> >>>>
>>> >>>> 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://www.twitter.com/openmicroscopy
>>> >>>>
>>> >>>>
>>> >>>>
>>> >>>>
>>> >>>>
>>> >>>>
>>> >>>> On 03/12/2014 16:06, "unai_lorenzo at ehu.es" <unai_lorenzo at ehu.es>
>>> >>>>wrote:
>>> >>>>
>>> >>>>
>>> >>>>> Dear OME users,
>>> >>>>>
>>> >>>>> I have just upgraded OMERO server from version 5.0.5 to 5.0.6.
>>> >>>>> OMERO.web seems to be working fine.
>>> >>>>> I could log in as root and check the data:
>>> >>>>>
>>> >>>>> ============================================================
>>> >>>>> ==============
>>> >>>>> ======
>>> >>>>> OMERO Diagnostics 5.0.6-ice35-b53
>>> >>>>> ============================================================
>>> >>>>> ==============
>>> >>>>> ======
>>> >>>>>
>>> >>>>> Commands: java -version 1.7.0
>>> (/usr/bin/java)
>>> >>>>> Commands: python -V 2.7.6
>>> >>>>>(/usr/bin/python)
>>> >>>>> Commands: icegridnode --version 3.5.1
>>> >>>>> (/usr/bin/icegridnode)
>>> >>>>> Commands: icegridadmin --version 3.5.1
>>> >>>>> (/usr/bin/icegridadmin)
>>> >>>>> Commands: psql --version 9.3.5
>>> (/usr/bin/psql)
>>> >>>>>
>>> >>>>> Server: icegridnode running
>>> >>>>> Server: Blitz-0 active (pid = 2779,
>>> >>>>>enabled)
>>> >>>>> Server: DropBox active (pid = 2791,
>>> >>>>>enabled)
>>> >>>>> Server: FileServer active (pid = 2795,
>>> >>>>>enabled)
>>> >>>>> Server: Indexer-0 active (pid = 2803,
>>> >>>>>enabled)
>>> >>>>> Server: MonitorServer active (pid = 2814,
>>> >>>>>enabled)
>>> >>>>> Server: OMERO.Glacier2 active (pid = 2801,
>>> >>>>>enabled)
>>> >>>>> Server: OMERO.IceStorm active (pid = 2826,
>>> >>>>>enabled)
>>> >>>>> Server: PixelData-0 active (pid = 2802,
>>> >>>>>enabled)
>>> >>>>> Server: Processor-0 active (pid = 2820,
>>> >>>>>enabled)
>>> >>>>> Server: Tables-0 active (pid = 2823,
>>> >>>>>enabled)
>>> >>>>> Server: TestDropBox inactive (enabled)
>>> >>>>>
>>> >>>>> OMERO: SSL port 4064
>>> >>>>> OMERO: TCP port 4063
>>> >>>>>
>>> >>>>> Log dir: /home/omero/OMERO.server-5.0.6-ice35-b53/var/log
>>> exists
>>> >>>>>
>>> >>>>> Log files: Blitz-0.log 1.0 MB errors=5
>>> >>>>> warnings=49
>>> >>>>> Log files: DropBox.log 6.0 KB errors=1
>>> >>>>> warnings=1
>>> >>>>> Log files: FileServer.log 0.0 KB
>>> >>>>> Log files: Indexer-0.log 7.0 KB
>>> >>>>> Log files: MonitorServer.log 4.0 KB
>>> >>>>> Log files: OMEROweb.log 60.0 KB errors=5
>>> >>>>> warnings=12
>>> >>>>> Log files: OMEROweb_request.log 0.0 KB
>>> >>>>> Log files: PixelData-0.log 9.0 KB
>>> >>>>> Log files: Processor-0.log 4.0 KB
>>> >>>>> Log files: Tables-0.log 4.0 KB errors=0
>>> >>>>> warnings=1
>>> >>>>> Log files: TestDropBox.log n/a
>>> >>>>> Log files: master.err 4.0 KB errors=0
>>> >>>>> warnings=3
>>> >>>>> Log files: master.out 0.0 KB
>>> >>>>> Log files: Total size 1.61 MB
>>> >>>>>
>>> >>>>>
>>> >>>>> Environment:OMERO_HOME=(unset)
>>> >>>>> Environment:OMERO_NODE=(unset)
>>> >>>>> Environment:OMERO_MASTER=(unset)
>>> >>>>> Environment:OMERO_TEMPDIR=(unset)
>>> >>>>> Environment:PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:
>>> >>>>> /usr/bin:/sbin:/
>>> >>>>> bin
>>> >>>>> Environment:PYTHONPATH=(unset)
>>> >>>>> Environment:ICE_HOME=(unset)
>>> >>>>> Environment:LD_LIBRARY_PATH=(unset)
>>> >>>>> Environment:DYLD_LIBRARY_PATH=(unset)
>>> >>>>>
>>> >>>>> OMERO data dir: '/home/omero/OMERO'Exists? TrueIs writable? True
>>> >>>>> OMERO temp dir: '/home/omero/omero/tmp'Exists? TrueIs writable?
>>> True
>>> >>>>> (Size: 0)
>>> >>>>> OMERO.web status... [RUNNING] (PID 3060)
>>> >>>>>
>>> >>>>>
>>> >>>>> Unfortunately OMERO.insight-5.0.6-ice35-b53 doesn't work using the
>>> >>>>> same settings (server IP address, username and password) I've been
>>> >>>>> using for OMERO.insight-5.0.5.
>>> >>>>>
>>> >>>>> Can anybody help me with this issue?
>>> >>>>> Many thanks in advance!
>>> >>>>>
>>> >>>>> Best regards,
>>> >>>>> Unai
>>> >>>>>
>>> >>>>> _______________________________________________
>>> >>>>> ome-users mailing list
>>> >>>>> ome-users at lists.openmicroscopy.org.uk
>>> >>>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>> >>>>>
>>> >>>>
>>> >>>>
>>> >>>> The University of Dundee is a registered Scottish Charity, No:
>>> >>>>SC015096
>>> >>>> Esta cabecera ha sido añadida automáticamente por la Vicegerencia de
>>> >>>>las
>>> >>>> TIC:
>>> >>>> ------------------------------------------------------------
>>> >>>> --------------------
>>> >>>> ATENCION!! Este correo contiene la palabra "contraseña" y puede
>>> >>>>tratarse
>>> >>>> de un fraude.
>>> >>>> No proporcione nunca sus credenciales por correo electrónico.
>>> >>>> Si tiene alguna duda consulte con el CAU (154400).
>>> >>>> UPV/EHU, Vicegerencia de las TIC
>>> >>>>
>>> >>>> ERNE!! Mezu honek "contraseña" hitza dauka eta iruzurrezko mezua
>>> izan
>>> >>>> daiteke.
>>> >>>> Ez eman inoiz zure pasahitza posta elektronikoaren bidez.
>>> >>>> Zalantzarik izanez gero deitu BAZren telefonora (154400)
>>> >>>> UPV/EHU, IKT Gerenteordetza
>>> >>>> ------------------------------------------------------------
>>> >>>> --------------------
>>> >>>> ·
>>> >>>>
>>> >>>
>>> >>>
>>> >>>
>>> >>> _______________________________________________
>>> >>> ome-users mailing list
>>> >>> ome-users at lists.openmicroscopy.org.uk
>>> >>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>> >>>
>>> >>>
>>> >>
>>> >> Esta cabecera ha sido añadida automáticamente por la Vicegerencia de
>>> >>las TIC:
>>> >>
>>> >>----------------------------------------------------------
>>> ---------------
>>> >>-------
>>> >> ATENCION!! Este correo contiene la palabra "contraseña" y puede
>>> >> tratarse de un fraude.
>>> >> No proporcione nunca sus credenciales por correo electrónico.
>>> >> Si tiene alguna duda consulte con el CAU (154400).
>>> >> UPV/EHU, Vicegerencia de las TIC
>>> >>
>>> >> ERNE!! Mezu honek "contraseña" hitza dauka eta iruzurrezko mezua
>>> >> izan daiteke.
>>> >> Ez eman inoiz zure pasahitza posta elektronikoaren bidez.
>>> >> Zalantzarik izanez gero deitu BAZren telefonora (154400)
>>> >> UPV/EHU, IKT Gerenteordetza
>>> >>
>>> >>----------------------------------------------------------
>>> ---------------
>>> >>-------
>>> >> ·
>>> >
>>> >
>>> >
>>>
>>>
>>> The University of Dundee is a registered Scottish Charity, No: SC015096
>>> _______________________________________________
>>> ome-users mailing list
>>> ome-users at lists.openmicroscopy.org.uk
>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>>
>>>
>> Esta cabecera ha sido añadida automáticamente por la Vicegerencia de las
>> TIC:
>> ------------------------------------------------------------
>> --------------------
>> ATENCION!! Este correo contiene la palabra "contraseña" y puede tratarse
>> de un fraude.
>> No proporcione nunca sus credenciales por correo electrónico.
>> Si tiene alguna duda consulte con el CAU (154400).
>> UPV/EHU, Vicegerencia de las TIC
>>
>> ERNE!! Mezu honek "contraseña" hitza dauka eta iruzurrezko mezua izan
>> daiteke.
>> Ez eman inoiz zure pasahitza posta elektronikoaren bidez.
>> Zalantzarik izanez gero deitu BAZren telefonora (154400)
>> UPV/EHU, IKT Gerenteordetza
>> ------------------------------------------------------------
>> --------------------
>> ·
>>
>
>
>
>
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