[ome-users] Making Omero work with Ice
Paulo Almeida
palmeida at igc.gulbenkian.pt
Fri Mar 27 11:15:09 GMT 2009
Hi Chris,
Thanks, that was the problem. I forgot I had to rebuild after 'svn up'.
That log was from an omero3.2 server I set up just for tests, but it's not
important now that I built omero4. Now bin/omero db script worked and I
created the database with
psql omero4 -U omero -h localhost < OMERO4__0.sql
but when I run
bin/omero admin start
it still fails. I am attaching the logs, but this bit doesn't seem good:
Caused by: org.postgresql.util.PSQLException: FATAL: password authentication
failed for user "omero"
Is it getting the database user and password from etc/omero.properties? I
think that is correctly set, and
psql -U omero -h localhost omero4
works, with password omero, which is what I put in etc/local.properties and
etc/omero.properties .
Thank you,
Paulo
On Thursday 26 March 2009 20:42:06 Chris Allan wrote:
> Hi Paulo,
>
> Something seems very wonky here. r4134 is OMERO Trunk and "db script"
> has been present for a while. Also, the Beta4 series does not use
> JBoss so is that server.log from your production installation?
>
> I'd start from "scratch" on your test OMERO checkout by running:
>
> * ./build.py clean ; ./build.py
> * cd dist
> * bin/omero db script
>
> and then see where we are.
>
> Ciao.
>
> -Chris
>
> On 26 Mar 2009, at 20:00, Paulo Almeida wrote:
> > Hi Josh,
> >
> > Thank you very much for the instructions. Regarding your questions,
> > I saw the
> > adduser option when I ran /bin/omero admin with no argument. That
> > returns
> > usage instructions that include 'adduser' as an option. Command line
> > addition
> > is not important to us, I was trying that because I thought it was
> > the only
> > way.
> >
> > But now I'm not sure I'm using the right version. I have been using
> > svn and
> > just did 'svn up' (at revision 4134), but when I tried:
> >
> > bin/omero db script
> >
> > I got:
> >
> > Unknown command: db script
> >
> > Running bin/omero without arguments and typing '?' gives me this
> > list of
> > commands:
> >
> > admin
> > config
> > download
> > help
> > load
> > node
> > quit
> > script
> > server
> > setup
> > submit
> > upload
> > version
> >
> > The version is "OmeroCli client, version 1.0".
> >
> > I also tried installing omero3.2 and I get the same error when
> > creating the
> > session within an omero script:
> >
> > Traceback (most recent call last):
> > File "<stdin>", line 1, in <module>
> > File "/home/palmeida/OMERO_test/OMERO/dist/lib/omero/__init__.py",
> > line 334,
> > in createSession
> > prx = self.getRouter(self.__ic).createSession(username, password)
> > File "/var/lib/python-support/python2.5/Glacier2_Router_ice.py",
> > line 104,
> > in createSession
> > return _M_Glacier2.Router._op_createSession.invoke(self, ((userId,
> > password), _ctx))
> > Ice.ConnectionRefusedException: Ice.ConnectionRefusedException:
> > Connection refused
> >
> > I am attaching omero-Beta3.2/jboss-4.2.3.GA/server/default/log/
> > server.log in
> > case it may help understand that error.
> >
> > Thanks again,
> > Paulo
> >
> > On Thursday 26 March 2009 18:07:44 you wrote:
> >> Paulo Almeida writes:
> >>> Hello,
> >>
> >> Hi Paulo.
> >>
> >>> Unfortunately I got stuck again... After running 'bin/omero admin
> >>> start'
> >>> and 'bin/omero admin deploy', when I run 'bin/omero admin status'
> >>> I get:
> >>>
> >>> palmeida at polyhymnia:~/OMERO_test/OMERO/dist$ bin/omero admin status
> >>> node is up
> >>> Server not reachable
> >>
> >> Hmmmm.....ok. That could be various things. Could you send us the
> >> var/log/* files?
> >>
> >>> Running 'bin/omero admin adduser' displays the usage help message
> >>> for
> >>> the omero command and trying the script in
> >>
> >> adduser got taken out of this release for lack of testing. Can you
> >> point me to where you found it listed in the documentation so I can
> >> quietly delete it? :)
> >>
> >>> http://trac.openmicroscopy.org.uk/omero/wiki/OmeroGrid
> >>>
> >>> returns an error after 'sf = c.createSession()'
> >>>
> >>>>>> sf = c.createSession()
> >>>
> >>> Traceback (most recent call last):
> >>> File "<stdin>", line 1, in <module>
> >>> File "/home/palmeida/OMERO_test/OMERO/dist/lib/omero/__init__.py",
> >>> line 334, in createSession
> >>> prx = self.getRouter(self.__ic).createSession(username, password)
> >>> File "/var/lib/python-support/python2.5/Glacier2_Router_ice.py",
> >>> line
> >>> 104, in createSession
> >>> return _M_Glacier2.Router._op_createSession.invoke(self,
> >>> ((userId,
> >>> password), _ctx))
> >>> Glacier2.PermissionDeniedException:
> >>> exception ::Glacier2::PermissionDeniedException
> >>> {
> >>> reason = internal server error
> >>> }
> >>
> >> This is most likely that your database is not properly configured.
> >> But
> >> the logs would tell us.
> >>
> >>> But I guess that is expected if the server is unreachable and I
> >>> can't
> >>> add users. Do you have any idea why this would happen? I checked
> >>> that
> >>> postgre is running and the database omero4 exists and is owned by
> >>> omero,
> >>> but it is empty:
> >>>
> >>> omero4=> \d
> >>> No relations found.
> >>
> >> Aha. Cancel the logs, that would be the problem.
> >>
> >>> Shouldn't the deploy command create the tables?
> >>
> >> No. The deploy command -- which is no longer necessary by the way --
> >> deploys the definition of your grid, i.e. etc/grid/default.xml. It
> >> defines which processes will be started and what properties they
> >> receive. It doesn't do anything with the database, since that
> >> persists
> >> longer than a single server start. (When I say deploy is no longer
> >> necessary, I mean that a deploy happens automatically every time you
> >> call "bin/omero admin start" so only if you want to change the
> >> configuration of a running grid do you need "deploy".)
> >>
> >> Now, we're hard at work on the release documentation and they're
> >> *almost*
> >> done, but for now you'll need to look at the RC1 email I sent:
> >>
> >>
> >> http://lists.openmicroscopy.org.uk/pipermail/ome-devel/2009-March/001184
> >>.ht ml
> >>
> >> for how to create your database. In summary, your next steps are:
> >>
> >> bin/omero db script
> >>
> >> which creates OMERO4__0.sql. If you haven't added the PLPGSQL
> >> language
> >> to your database, then you'll need to:
> >>
> >> createlang plpgsql omero4
> >>
> >> and finally:
> >>
> >> psql omero4 < OMERO4__0.sql
> >> bin/omero admin stop
> >> bin/omero admin start
> >>
> >> For 4.0.0 use the webadmin panel at: http://localhost:8000/webadmin
> >> to
> >> add new users. If the command-line addition is of interest, we'll
> >> certainly have that re-scheduled for an upcoming release.
> >>
> >>> Thanks,
> >>> Paulo
> >>
> >> No problem and cheers,
> >> ~Josh
> >>
> >>> On Wednesday 25 March 2009 19:23:11 you wrote:
> >>>> Paulo Almeida writes:
> >>>>> Hi again...
> >>>>>
> >>>>> Ignore my last e-mail, it really was a simple permissions problem.
> >>>>> I didn't think it was because I tried running as root, but the
> >>>>> directory was mounted in NFS so root didn't have access either. It
> >>>>> seems to be running fine now.
> >>>>
> >>>> Whew. Good to hear! :) Thanks for letting us know, Paulo.
> >>>>
> >>>> ~J.
> >>>>
> >>>>> Best,
> >>>>> Paulo
> >>>>>
> >>>>> On Wednesday 25 March 2009 18:04:11 Paulo Almeida wrote:
> >>>>>> Hi,
> >>>>>>
> >>>>>> I had an OmeroGrid installation that was working, but I had to
> >>>>>> reinstall the OS and now I am getting an error. When I run:
> >>>>>>
> >>>>>> bin/omero admin start
> >>>>>>
> >>>>>> there is not output, but then I run:
> >>>>>>
> >>>>>> bin/omero admin deploy etc/grid/default.xml
> >>>>>>
> >>>>>> and I get this:
> >>>>>>
> >>>>>> error: IceGrid::DeploymentException:
> >>>>>> couldn't load `Blitz-0' on node `master':
> >>>>>> can't set permissions on directory
> >>>>>> `/mnt/OMERO_test/OMERO/dist/var/master/servers/Blitz-0'
> >>>>>>
> >>>>>> -----------
> >>>>>>
> >>>>>> When I reinstalled the OS I had to install Ice, PostgreSQL, etc,
> >>>>>> but I didn't touch the Omero folder. Do you have any idea about
> >>>>>> what I may have forgotten that would cause this error? I also
> >>>>>> tried compiling Omero.blitz, but I get this error when running
> >>>>>> 'bin/omero admin start':
> >>>>>>
> >>>>>> icegridnode: failure occurred in daemon:
> >>>>>> service caught unhandled Ice exception:
> >>>>>> ../../include/Ice/BasicStream.h:412:
> >>>>>> Ice::UnmarshalOutOfBoundsException: protocol error: out of bounds
> >>>>>> during unmarshaling
> >>>>>> from /mnt/OMERO_test/OMERO_blitz/dist/var/log/master.err:
> >>>>>> ../../include/Ice/BasicStream.h:412:
> >>>>>> Ice::UnmarshalOutOfBoundsException: protocol error: out of bounds
> >>>>>> during unmarshaling
> >
> > <server.log>_______________________________________________
> > ome-users mailing list
> > ome-users at lists.openmicroscopy.org.uk
> > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
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