[ome-users] Initialize the OMERO database
Zoltan Cseresnyes
zcseresn at gmail.com
Tue Apr 14 15:15:31 BST 2009
Stuart,
What does the master error file say? On Linux I just installed OMERO4 over
the weekend and had the same error message for a while. When I looked into
the "master.err" file (not sure where it is on Windows, but on Linux it's in
/omero-Beta4.0.0/var/log/), it said that the icegrid registry was already
running and listening at port 4061. I had to restart the OS and then it was
fine. Apparently, with admin stop, you are not stopping the ice server. I
hope I'm correct here and that it helps you a bit.
Zoltan
On Tue, Apr 14, 2009 at 2:33 PM, Smith, Stuart C
<Stuart.C.Smith at pfizer.com>wrote:
> Hi Colin, no worries as if everything ran smoothly, we wouldn't learn
> anything :o)
>
> find the requested info...
>
> C:\omero-Beta4.0.0>bin\omero config get
> omero.data.dir='D:\\OMERO'
> omero.db.name=omero
> omero.db.pass=omero
> omero.db.user=omero
>
> C:\omero-Beta4.0.0>bin\omero config set omero.data.dir
> 'C:\OMERO'
>
> C:\omero-Beta4.0.0>bin\omero config get
> omero.data.dir='C:\OMERO'
> omero.db.name=omero
> omero.db.pass=omero
> omero.db.user=omero
>
> I noticed the data.dir was pointing to a non-existant D:\ Drive,
> although I'm sure I changed it (but can't have) and therefore configured
> to C:\
>
> I then stopped & restarted the server with "bin\omero admin start"
>
> C:\omero-Beta4.0.0>bin\omero admin stop
>
> SERVICE_NAME: OMERO.master
> TYPE : 10 WIN32_OWN_PROCESS
> STATE : 4 RUNNING
>
> (STOPPABLE,NOT_PAUSABLE,ACCEPTS_SHUTDOWN)
> WIN32_EXIT_CODE : 0 (0x0)
> SERVICE_EXIT_CODE : 0 (0x0)
> CHECKPOINT : 0x0
> WAIT_HINT : 0x0
>
> [SC] DeleteService SUCCESS
>
> Waiting on shutdown. Use CTRL-C to exit
> icegridadmin: could not contact the default locator:
> Network.cpp:1218: Ice::ConnectionRefusedException:
> connection refused: WSAECONNREFUSED
>
>
>
> C:\omero-Beta4.0.0>bin\omero admin start
> No descriptor given. Using etc/grid/default.xml
> [SC] CreateService SUCCESS
>
> SERVICE_NAME: OMERO.master
> TYPE : 10 WIN32_OWN_PROCESS
> STATE : 2 START_PENDING
>
> (NOT_STOPPABLE,NOT_PAUSABLE,IGNORES_SHUTDOWN)
> WIN32_EXIT_CODE : 0 (0x0)
> SERVICE_EXIT_CODE : 0 (0x0)
> CHECKPOINT : 0x0
> WAIT_HINT : 0x7d0
> PID : 1004
> FLAGS :
>
> Waiting on startup. Use CTRL-C to exit
> icegridadmin: could not contact the default locator:
> Network.cpp:1218: Ice::ConnectionRefusedException:
> connection refused: WSAECONNREFUSED
> .
> C:\omero-Beta4.0.0>
>
>
> Stuart
>
>
> -----Original Message-----
> From: Colin Blackburn [mailto:c.blackburn at dundee.ac.uk]
> Sent: 14 April 2009 14:15
> To: Smith, Stuart C
> Cc: ome-users at lists.openmicroscopy.org.uk
> Subject: Re: [ome-users] Initialize the OMERO database
>
> Hi Stuart,
>
> sorry to hear you are having problems with Windows, it seems to throw up
>
> a few interesting issues on some machines and not on others.
>
> Can you let me know what the response is to:
>
> C:\omero-Beta4.0.0>bin\omero config get
>
> And, what your omero data directory actually is?
>
> Cheers,
>
> Colin
>
>
> Smith, Stuart C wrote:
> > Hi, for "stop" I get...
> >
> > C:\omero-Beta4.0.0>bin\omero admin stop
> >
> > SERVICE_NAME: OMERO.master
> > TYPE : 10 WIN32_OWN_PROCESS
> > STATE : 4 RUNNING
> > (STOPPABLE,NOT_PAUSABLE,ACCEPTS_SHUTDO
> > WIN32_EXIT_CODE : 0 (0x0)
> > SERVICE_EXIT_CODE : 0 (0x0)
> > CHECKPOINT : 0x0
> > WAIT_HINT : 0x0
> >
> > [SC] DeleteService SUCCESS
> >
> > Waiting on shutdown. Use CTRL-C to exit
> > icegridadmin: could not contact the default locator:
> > Network.cpp:1218: Ice::ConnectionRefusedException:
> > connection refused: WSAECONNREFUSED
> >
> > and when I restart, I get...
> >
> > C:\omero-Beta4.0.0>bin\omero admin start
> > No descriptor given. Using etc/grid/default.xml
> > [SC] CreateService SUCCESS
> >
> >
> > SERVICE_NAME: OMERO.master
> > TYPE : 10 WIN32_OWN_PROCESS
> > STATE : 2 START_PENDING
> >
> > (NOT_STOPPABLE,NOT_PAUSABLE,IGNORES_SHUTDOWN)
> > WIN32_EXIT_CODE : 0 (0x0)
> > SERVICE_EXIT_CODE : 0 (0x0)
> > CHECKPOINT : 0x0
> > WAIT_HINT : 0x7d0
> > PID : 3412
> > FLAGS :
> >
> > Waiting on startup. Use CTRL-C to exit
> > icegridadmin: could not contact the default locator:
> > Network.cpp:1218: Ice::ConnectionRefusedException:
> > connection refused: WSAECONNREFUSED
> > .
> > C:\omero-Beta4.0.0>
> >
> > Thanks in advance,
> >
> > Stu
> >
> >
> > -----Original Message-----
> > From: ome-users-bounces at lists.openmicroscopy.org.uk
> > [mailto:ome-users-bounces at lists.openmicroscopy.org.uk] On Behalf Of
> > Paulo Almeida
> > Sent: 14 April 2009 13:31
> > To: ome-users at lists.openmicroscopy.org.uk
> > Subject: Re: [ome-users] Initialize the OMERO database
> >
> > Hi Stuart,
> >
> > If you haven't done that yet, I would try:
> >
> > bin\omero admin stop
> >
> > and then:
> >
> > bin\omero admin start
> >
> > Good luck,
> > Paulo
> >
> > On Tuesday 14 April 2009 12:24:26 Smith, Stuart C wrote:
> >> Hi Josh, thanks for that. I have now downgraded to ICE 3.3.0 and
> upon
> >> running the "start sever" command I get...
> >>
> >> C:\omero-Beta4.0.0>bin\omero admin start
> >> No descriptor given. Using etc/grid/default.xml
> >> [SC] StartService FAILED 1056:
> >>
> >> An instance of the service is already running.
> >>
> >> Waiting on startup. Use CTRL-C to exit
> >>
> >> C:\omero-Beta4.0.0>
> >>
> >> I guess, trying not to state the obvious, that the required services
> > are
> >> already running. Of which, I have checked & the "postgreSQ" & "OMERO
> >> Master" services are both running.
> >>
> >> But when I try to view the webadmin page, it cannot be displayed.
> Any
> >> idea's?
> >>
> >> Stuart
> >>
> >>
> >> p.s. I will be installing 4.0.1 upon release, but by trying to get
> > 4.0.0
> >> working its helping me understand the app :o)
> >>
> >>
> >> -----Original Message-----
> >> From: josh.moore at gmx.de [mailto:josh.moore at gmx.de]
> >> Sent: 09 April 2009 15:23
> >> To: Smith, Stuart C; ome-users at lists.openmicroscopy.org.uk
> >> Subject: Re: [ome-users] Initialize the OMERO database
> >>
> >> Smith, Stuart C writes:
> >> > Hi Josh,
> >>
> >> Hi Stuart,
> >>
> >> > Anyway, with your help I sorted that that. I know you mentioned
> >>
> >> that
> >>
> >> > 4.0.1 will be released soon, but i decided to carry on with 4.0 as
> > a
> >> > test installation until 4.0.1 in available. Everything else went
> > ok,
> >> > until i tried to start the server and got the below error...
> >> >
> >> > ...
> >> > No descriptor given. Using etc/grid/default.xml
> >> > [SC] StartService FAILED 3:
> >> >
> >> > The system cannot find the path specified.
> >> >
> >> > Waiting on startup. Use CTRL-C to exit
> >> > icegridadmin: could not contact the default locator:
> >> > Network.cpp:1220: Ice::ConnectionRefusedException:
> >> > connection refused: WSAECONNREFUSED
> >> >
> >> > Any ideas?
> >>
> >> This is one of the errors fixed in 4.0.1. Though your best bet is to
> >> wait for the release, I can give you a quick tip and you can go from
> >> there: if you've installed Ice-3.3.1 which you probably have, move it
> >> to C:\Ice-3.3.0 since the path is hard-coded. In the upcoming
> release,
> >> it's not hard-coded, but after install it requires a reboot. Those
> are
> >> the types of trade-offs in this business. :)
> >>
> >> Best wishes,
> >> ~Josh.
> >>
> >> > Thanks,
> >> >
> >> > Stuart
> >> >
> >> >
> >> > -----Original Message-----
> >> > From: josh.moore at gmx.de [mailto:josh.moore at gmx.de]
> >> > Sent: 08 April 2009 19:09
> >> > To: Smith, Stuart C
> >> > Cc: ome-users at lists.openmicroscopy.org.uk
> >> > Subject: [ome-users] Initialize the OMERO database
> >> >
> >> >
> >> > Hi Stuart,
> >> >
> >> > before I begin a minor warning, we'll be releasing 4.0.1 in the
> > next
> >> > day or two with improved Windows support. So, though it doesn't
> >>
> >> change
> >>
> >> > any of the instructions for getting your database setup, it may
> > make
> >> > sense to wait for the final installation until then.
> >> >
> >> > But first, your db...
> >> >
> >> > Smith, Stuart C writes:
> >> > > Hi, I'm sure this will be a very basic question to most of you
> > but
> >> > > I have been asked to set up a PC running the OMERO server
> >> > > installation and have followed the Windows installation
> document
> >> > > upto the point where you are asked to "Initialize the OMERO
> >> > > database" with the script...
> >> > >
> >> > > $ cd C:\omero-Beta4.0.0\
> >> > > $ bin\omero db script
> >> > > Please enter omero.db.version [OMERO4]:
> >> > > Please enter omero.db.patch [0]:
> >> > > Please enter password for new OMERO root user:
> >> > > Please re-enter password for new OMERO root user:
> >> > > Saving to C:\omero-Beta4.0.0\OMERO4__0.sql
> >> > > $
> >> > >
> >> > > But have tried pasting into a cmd window, but it doesn't like
> > it.
> >> I
> >>
> >> > > therefore tried the first line & realised that it wasn't even
> >> >
> >> > changing
> >> >
> >> > > directories, therefore removed the 1st "$" char & that worked,
> > but
> >> >
> >> > then
> >> >
> >> > > got stuck on the 2nd line. Can someone please help me
> > initialize
> >> the
> >>
> >> > > DB.
> >> >
> >> > The dollar signs are a copy-n-paste issue from the non-Windows
> >> > instructions. Sorry about that. I've fixed them in the
> > documentation
> >> > for the coming release.
> >> >
> >> > > Also, as I was unsure if it had worked, although I wasn't
> > prompted
> >> >
> >> > for
> >> >
> >> > > the password as I added it to the script manually so I tried
> the
> >>
> >> next
> >>
> >> > > step of populating the database by copying the script in the
> >> > > installation document into "SQL Shell (psql)" and this errored,
> >>
> >> but
> >>
> >> > was
> >> >
> >> > > this because I hadn't initialized the db?
> >> > >
> >> > > Any help you guys can offer would be great as I have been asked
> > to
> >> >
> >> > set
> >> >
> >> > > this up to see if the software is useful to us.
> >> >
> >> > Alright. I'm a bit lost in what you tried, and what did and didn't
> >> > work. What you should use to create your database script is:
> >> >
> >> > cd C:\omero-Beta4.0.0\
> >> > bin\omero db script
> >> >
> >> > Then you should be asked the questions about version and
> >> > password. You said you weren't asked for a password. That seems
> >> > odd. How did you go about adding that manually?
> >> >
> >> > Once you've done that, then opening the SQL Shell as mentioned in
> > the
> >> > docs is certainly correct. The statement "\i ... OMERO4__0.sql" is
> >>
> >> the
> >>
> >> > process of initializing your db, so that can't be why it errored.
> > Can
> >> > you send us the error that it produced?
> >> >
> >> > > Thanks in advance,
> >> > > Stuart
> >> >
> >> > Hope that helps somewhat.
> >> > Best wishes,
> >> > ~Josh.
> >>
> >> _______________________________________________
> >> ome-users mailing list
> >> ome-users at lists.openmicroscopy.org.uk
> >> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
> >
> >
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--
Zoltan Cseresnyes
Facility manager, Imaging Suite
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