[ome-users] OMERO.web installation under Ubuntu 14
unai_lorenzo at ehu.es
unai_lorenzo at ehu.es
Thu Oct 2 12:09:40 BST 2014
Dear Simon,
I symlinked the 'nginx.conf.template' file to the
'/etc/nginx/sites-enabled' folder, restarted nginx, and I couldn't
success once again.
Appart from that I've also tried to login from OMERO.insight, and I
couldn't run the 'OMEROinsight_unix.sh' file from the terminal due to
an abnormal termination:
Abnormal termination due to an uncaught exception.
java.awt.HeadlessException
at java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:207)
at java.awt.Window.<init>(Window.java:535)
at java.awt.Frame.<init>(Frame.java:420)
at javax.swing.JFrame.<init>(JFrame.java:218)
at
org.openmicroscopy.shoola.util.ui.login.ScreenLogin.<init>(ScreenLogin.java:1033)
at
org.openmicroscopy.shoola.env.ui.SplashScreenManager.initializedView(SplashScreenManager.java:176)
at
org.openmicroscopy.shoola.env.ui.SplashScreenManager.<init>(SplashScreenManager.java:241)
at
org.openmicroscopy.shoola.env.ui.SplashScreenProxy.<init>(SplashScreenProxy.java:123)
at
org.openmicroscopy.shoola.env.ui.UIFactory.makeSplashScreen(UIFactory.java:59)
at
org.openmicroscopy.shoola.env.init.SplashScreenInit.execute(SplashScreenInit.java:99)
at
org.openmicroscopy.shoola.env.init.Initializer.doInit(Initializer.java:276)
at
org.openmicroscopy.shoola.env.Container.runStartupProcedure(Container.java:128)
at org.openmicroscopy.shoola.env.Container.access$000(Container.java:78)
at org.openmicroscopy.shoola.env.Container$1.run(Container.java:174)
at java.lang.Thread.run(Thread.java:745)
Exception in thread "Initializer"
Exception: java.awt.HeadlessException thrown from the
UncaughtExceptionHandler in thread "Initializer"
Maybe this error is related to the connection problems, or maybe this
is an extra problem...
Thanks,
Unai
Simon Li <s.p.li at dundee.ac.uk> escribió:
> Hi Unai
>
> /etc/nginx is a system directory on the server's root partition, it's
> not part of OMERO.server.
>
> Simon
>
> On Wed, 2014-10-01 at 18:11 +0200, unai_lorenzo at ehu.es wrote:
>> Hi Simon,
>>
>> Maybe that's the problem...
>> While I was following the installation protocol I skipped that step
>> because I didn't find any folder called '/nginx'. The only folders
>> included in the '/etc' directory are '/etc/grid' and '/etc/profiles'.
>>
>> Could you please tell me when and how this folder is generated ?
>>
>> Cheers,
>> Unai
>>
>> Simon Li <s.p.li at dundee.ac.uk> escribió:
>>
>> > Can I just check you copied or symlinked the config to
>> > /etc/nginx/sites-enabled, and restarted nginx?
>> >
>> > Simon
>> >
>> > On 01/10/2014 11:52, "unai_lorenzo at ehu.es" <unai_lorenzo at ehu.es> wrote:
>> >
>> >> Hi Simon,
>> >> I'm using Ubuntu 14.04 LTS.
>> >>
>> >> I've been following OMERO.server installation
>> >>
>> (http://www.openmicroscopy.org/site/support/omero5/sysadmins/unix/server-i
>> >> nstallation.html), OMERO.server Linux walkthrough
>> >>
>> (http://www.openmicroscopy.org/site/support/omero5/sysadmins/unix/server-l
>> >> inux-walkthrough.html), and OMERO.web deployment
>> >>
>> (http://www.openmicroscopy.org/site/support/omero5/sysadmins/unix/install-
>> >> web.html).
>> >>
>> >> I generated the nginx configuration with 'bin/omero web config nginx
>> >> --system'.
>> >> The first lines that the command returned are:
>> >> listen 8080;
>> >> server_name $hostname;
>> >>
>> >>
>> >> I installed nginx at the same time as Ice, Java and Postgres. I used
>> >> the following command (as suggested in the walkthrough):
>> >>
>> >> apt-get -y install \
>> >> unzip \
>> >> wget \
>> >> python-{imaging,matplotlib,numpy,pip,scipy,tables,virtualenv} \
>> >> openjdk-7-jre-headless \,
>> >> ice-services python-zeroc-ice \
>> >> postgresql \
>> >> nginx
>> >>
>> >> Thanks for your help,
>> >> Unai
>> >>
>> >> Simon Li <s.p.li at dundee.ac.uk> escribió:
>> >>
>> >>> Hi Unai
>> >>>
>> >>> What operating system and version are you using? Which set of
>> >>> instructions
>> >>> were you following- the ones from
>> >>>
>> >>>
>> https://www.openmicroscopy.org/site/support/omero5/sysadmins/unix/install
>> >>> -w
>> >>> eb.html or the walkthrough at
>> >>>
>> >>>
>> https://www.openmicroscopy.org/site/support/omero5/sysadmins/unix/server-
>> >>> li
>> >>> nux-walkthrough.html ?
>> >>>
>> >>> Did you generate your nginx config with 'bin/omero web config nginx
>> >>> --system’? And finally, how did you install this nginx config?
>> >>>
>> >>> Thanks
>> >>>
>> >>> Simon
>> >>>
>> >>> On 30/09/2014 16:25, "unai_lorenzo at ehu.es" <unai_lorenzo at ehu.es> wrote:
>> >>>
>> >>>> Hi Simon,
>> >>>>
>> >>>> Unluckily your suggestions didn't work either.
>> >>>>
>> >>>> When I try to access OMERO.web on port 80 I can see the following
>> >>>> message:
>> >>>> Welcome to nginx!
>> >>>> If you see this page, the nginx web server is successfully installed
>> >>>> and working. Further configuration is required.
>> >>>>
>> >>>> And if I try to access OMERO.web on port 8080 the address is not
>> >>>> valid. Does it mean that I should configure Apache or Nginx to listen
>> >>>> to 8080 port?
>> >>>>
>> >>>> Thanks again!!
>> >>>> Unai
>> >>>>
>> >>>>
>> >>>> Simon Li <s.p.li at dundee.ac.uk> escribió:
>> >>>>
>> >>>>> Hi Unai
>> >>>>>
>> >>>>> Could you try unsetting all of your omero.web.* configuration options,
>> >>>>> regenerate your nginx or apache configuration files, restart OMERO and
>> >>>>> OMERO.web, and seeing if that works?
>> >>>>>
>> >>>>> Thanks
>> >>>>>
>> >>>>> Simon
>> >>>>>
>> >>>>> On 30/09/2014 08:34, "unai_lorenzo at ehu.es" <unai_lorenzo at ehu.es>
>> >>>>> wrote:
>> >>>>>
>> >>>>>> Dear Simon,
>> >>>>>>
>> >>>>>> I'm using nginx/apache.
>> >>>>>> I've also tried to access OMERO.web on the ports you suggested but it
>> >>>>>> didn't work either.
>> >>>>>> This is the output of `bin/omero config get':
>> >>>>>>
>> >>>>>> omero.data.dir=/home/jribecarios/OMERO
>> >>>>>> omero.db.name=omero_database
>> >>>>>> omero.db.pass=db_password
>> >>>>>> omero.db.user=db_user
>> >>>>>> omero.web.application_server=fastcgi
>> >>>>>> omero.web.application_server.host=localhost
>> >>>>>> omero.web.application_server.port=4080
>> >>>>>> omero.web.force_script_name=/omero
>> >>>>>> omero.web.static_url=/omero/static/
>> >>>>>> jribecarios at jribecarios:~/omero/OMERO.server-5.0.4-ice35-b43$
>> >>>>>>
>> >>>>>>
>> >>>>>> I hope it helps.
>> >>>>>>
>> >>>>>> Many thanks,
>> >>>>>> Unai
>> >>>>>>
>> >>>>>>
>> >>>>>> Simon Li <s.p.li at dundee.ac.uk> escribió:
>> >>>>>>
>> >>>>>>> Hi Unai
>> >>>>>>>
>> >>>>>>> Are you using the development web server, or nginx/apache? If it¹s
>> >>>>>>> the
>> >>>>>>> latter then OMERO.web should be accessible on either port 80 or 8080
>> >>>>>>> depending on your configuration, port 4080 is used for internal
>> >>>>>>> communication.
>> >>>>>>>
>> >>>>>>> If this doesn¹t solve your problem could you paste the output of
>> >>>>>>> `bin/omero config get`?
>> >>>>>>>
>> >>>>>>> Thanks
>> >>>>>>>
>> >>>>>>> Simon
>> >>>>>>>
>> >>>>>>> On 29/09/2014 16:58, "unai_lorenzo at ehu.es" <unai_lorenzo at ehu.es>
>> >>>>>>> wrote:
>> >>>>>>>
>> >>>>>>>> Dear OME users,
>> >>>>>>>>
>> >>>>>>>> I am trying to install OMERO.web under Ubuntu 14. I've been
>> >>>>>>>> following
>> >>>>>>>> all the instructions included in the web page, and everything seems
>> >>>>>>>> to
>> >>>>>>>> be OK: I could start the server, and the OMERO.web client.
>> >>>>>>>>
>> >>>>>>>> $ bin/omero web start
>> >>>>>>>>
>> >>>>>>>> 0 static files copied, 816 unmodified.
>> >>>>>>>> Starting OMERO.web... [OK]
>> >>>>>>>>
>> >>>>>>>>
>> >>>>>>>> But I can't access OMERO.webadmin on the following address
>> >>>>>>>> http://localhost:4080.
>> >>>>>>>>
>> >>>>>>>> Any guess about what's wrong? Could it be the something related to
>> >>>>>>>> the
>> >>>>>>>> the firewall and the TCP ports?
>> >>>>>>>>
>> >>>>>>>>
>> >>>>>>>> Here you will find the diagnostics:
>> >>>>>>>>
>> >>>>>>>>
>> >>>>>>>>
>> >>>>>>>>
>> >>>>>>>>
>> ====================================================================
>> >>>>>>>> ==
>> >>>>>>>> ==
>> >>>>>>>> ==
>> >>>>>>>> ======
>> >>>>>>>> OMERO Diagnostics 5.0.4-ice35-b43
>> >>>>>>>>
>> >>>>>>>>
>> >>>>>>>>
>> >>>>>>>>
>> ====================================================================
>> >>>>>>>> ==
>> >>>>>>>> ==
>> >>>>>>>> ==
>> >>>>>>>> ======
>> >>>>>>>>
>> >>>>>>>> WARNING:omero.util.UpgradeCheck:UPGRADE AVAILABLE:Please upgrade to
>> >>>>>>>> 5.0.5 See http://trac.openmicroscopy.org.uk/omero for the latest
>> >>>>>>>> version
>> >>>>>>>>
>> >>>>>>>> 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 = 4371,
>> >>>>>>>> enabled)
>> >>>>>>>> Server: DropBox active (pid = 4403,
>> >>>>>>>> enabled)
>> >>>>>>>> Server: FileServer active (pid = 4404,
>> >>>>>>>> enabled)
>> >>>>>>>> Server: Indexer-0 active (pid = 4383,
>> >>>>>>>> enabled)
>> >>>>>>>> Server: MonitorServer active (pid = 4387,
>> >>>>>>>> enabled)
>> >>>>>>>> Server: OMERO.Glacier2 active (pid = 4394,
>> >>>>>>>> enabled)
>> >>>>>>>> Server: OMERO.IceStorm active (pid = 4420,
>> >>>>>>>> enabled)
>> >>>>>>>> Server: PixelData-0 active (pid = 4410,
>> >>>>>>>> enabled)
>> >>>>>>>> Server: Processor-0 active (pid = 4416,
>> >>>>>>>> enabled)
>> >>>>>>>> Server: Tables-0 active (pid = 4412,
>> >>>>>>>> enabled)
>> >>>>>>>> Server: TestDropBox inactive (enabled)
>> >>>>>>>>
>> >>>>>>>> OMERO: SSL port 4064
>> >>>>>>>> OMERO: TCP port 4063
>> >>>>>>>>
>> >>>>>>>> Log dir:
>> >>>>>>>> /home/jribecarios/omero/OMERO.server-5.0.4-ice35-b43/var/log exists
>> >>>>>>>>
>> >>>>>>>> Log files: Blitz-0.log 672.0 KB errors=12
>> >>>>>>>> warnings=6
>> >>>>>>>> Log files: DropBox.log 3.0 KB errors=0
>> >>>>>>>> warnings=1
>> >>>>>>>> Log files: FileServer.log 0.0 KB
>> >>>>>>>> Log files: Indexer-0.log 21.0 KB errors=13
>> >>>>>>>> warnings=0
>> >>>>>>>> Log files: MonitorServer.log 2.0 KB
>> >>>>>>>> Log files: OMEROweb.log 0.0 KB
>> >>>>>>>> Log files: OMEROweb_request.log 0.0 KB
>> >>>>>>>> Log files: PixelData-0.log 25.0 KB errors=18
>> >>>>>>>> warnings=1
>> >>>>>>>> Log files: Processor-0.log 2.0 KB errors=0
>> >>>>>>>> warnings=1
>> >>>>>>>> Log files: Tables-0.log 2.0 KB
>> >>>>>>>> Log files: TestDropBox.log n/a
>> >>>>>>>> Log files: master.err 2.0 KB errors=0
>> >>>>>>>> warnings=4
>> >>>>>>>> Log files: master.out 0.0 KB
>> >>>>>>>> Log files: Total size 0.73 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:/
>> >>>>>>>> sb
>> >>>>>>>> in
>> >>>>>>>> :/
>> >>>>>>>> bin:/usr/games:/usr/local/games
>> >>>>>>>> Environment:PYTHONPATH=(unset)
>> >>>>>>>> Environment:ICE_HOME=(unset)
>> >>>>>>>> Environment:LD_LIBRARY_PATH=(unset)
>> >>>>>>>> Environment:DYLD_LIBRARY_PATH=(unset)
>> >>>>>>>>
>> >>>>>>>> OMERO data dir: '/home/jribecarios/OMERO'Exists? TrueIs writable?
>> >>>>>>>> True
>> >>>>>>>> OMERO temp dir: '/home/jribecarios/omero/tmp'Exists? TrueIs
>> >>>>>>>> writable? True (Size: 0)
>> >>>>>>>> OMERO.web status... [RUNNING] (PID 11366)
>> >>>>>>>>
>> >>>>>>>>
>> >>>>>>>> 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
>> >>>>>>
>> >>>>>>
>> >>>>>>
>> >>>>>
>> >>>>>
>> >>>>> 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
>> >>>>>
>> >>>>>
>> >>>>>
>> -----------------------------------------------------------------------
>> >>>>> --
>> >>>>> -------
>> >>>>> ·
>> >>>>
>> >>>>
>> >>>>
>> >>>
>> >>>
>> >>> 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
>> >
>> >
>> > 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
>> >
>> --------------------------------------------------------------------------------
>> > ·
>>
>>
>>
>
>
> 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
> --------------------------------------------------------------------------------
> ·
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