[ome-users] Making Omero work with Ice

[josh.moore at gmx.de]

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.html

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
 >