[ome-users] Omero Beta 4 installation problems

[josh.moore at gmx.de]

Chris Roome writes:
 > Hi all,

Hi Chris,

 > I would be very grateful for any help with my attempts to install Omera
 > 4 please! Sorry for the long e-mail.

No worries. Rather a long email than lots of short ones! :)

 > I have been trying to install the beta 4 release on our linux server,
 > it's an OpenSuSE 10.1 system (2.6.16.21-0.25-smp x86_64). It is a clean
 > install (several times).
 > 
 > The postgreSQL (v8.3.3) installation was OK, java is installed
 > (jdk1.5.0_11), as is ICE (v3.3.1) and python (v2.4.2).
 > 
 > I followed through the all the installation instructions, but when I
 > start the server, I get this:
 > 
 > local/omero-Beta4.0.0> bin/omero admin start
 > No descriptor given. Using etc/grid/default.xml
 > Waiting on startup. Use CTRL-C to exit
 > ................
 > 
 > with the cursor moving across the shell (i.e. doesn't drop back to the
 > prompt).
 > 
 > Looking at the processes, I see that this process is being re-started
 > every second or so:
 > 
 > icegridadmin --Ice.Config=/usr/local/omero-Beta4.0.0/etc/internal.cfg -e
 > node ping master
 > 
 > It keeps re-trying until I ctrl-c the '... admin start' from the shell.

Right. In the latest version we've added a timeout of 5 minutes, but
it's expected that icegridadmin will be called periodically, with the
hope that your server comes up.

 > If I try to run this command directly from the shell, I get:
 > 
 > local/omero-Beta4.0.0> icegridadmin
 > --Ice.Config=/usr/local/omero-Beta4.0.0/etc/internal.cfg -e node ping master
 > icegridadmin: too many arguments

You need to add quotes here:  ... -e "node ping master"

 > but from 'omero admin ice':
 > 
 > local/omero-Beta4.0.0> bin/omero admin ice
 > Ice 3.3.1  Copyright 2003-2009 ZeroC, Inc.
 > >>> node ping master
 > node is up
 > >>>

Right. This means that the second check of `bin/omero admin status` is
failing, which tries to connect to the server.

 > The Omera binary repository and omero server installation directory have
 > read/write/execute permission (for all at the moment, for testing).
 > 
 > The django web server starts, and I can see the OME login window from
 > http://localhost:8000/WebAdmin but I cannot log in ("Error:
 > PermissionDeniedException").

This also means that your server isn't running.

 > Below, I have copied and pasted some of the error messages in the
 > various ../var/log files (sorry for the long e-mail!) and a listing of
 > the running processes.

Great. Thanks. This is the bit that's getting you:

 > 2009-04-07 16:41:38,046 ERROR [ome.services.db.SelfCorrectingDataSource]
 > (      main) Failed to acquire connection after retries=3
 > java.sql.SQLException: unable to get a connection from pool of a
 > PoolingDataSource containing an XAPool of resource
 > 6046fc17-e86a-4705-8b4a-1790059947ab with 0 connec

Your database is not reachable. Did you do any extra configuration? If
so, what does `bin/omero config get` look like? Does `psql -U omero -h
localhost omero` (or your values for those properties) work?

Hope that helps.
~Josh.




 > running processes (after ctrl-c) from '... admin start':
 > 
 > my-user    20232     1  0 17:54 ?        00:00:00 icegridnode --daemon
 > --pidfile /usr/local/omero-Beta4.0.0/var/master/master.pid --nochdir
 > --Ice.Config=/usr/local/omero-Beta4.0.0/etc/internal.cfg,/usr/local/omero-Beta4.0.0/etc/master.cfg
 > --deploy /usr/local/omero-Beta4.0.0/etc/grid/default.xml
 > 
 > my-user    20313 20232  0 17:54 ?        00:00:00 python
 > lib/python/fsRunFSServer.py
 > --Ice.Config=/usr/local/omero-Beta4.0.0/var/master/servers/FSServer/config/config
 > 
 > my-user    20315 20232  0 17:54 ?        00:00:00 glacier2router
 > --Ice.Config=/usr/local/omero-Beta4.0.0/var/master/servers/OMERO.Glacier2/config/config
 > 
 > my-user    20322 20232  0 17:54 ?        00:00:00 icebox
 > --Ice.Config=/usr/local/omero-Beta4.0.0/var/master/servers/OMERO.IceStorm/config/config
 > 
 > my-user    20325 20232  0 17:54 ?        00:00:00 python
 > lib/python/shellserver.py Web
 > --Ice.Config=/usr/local/omero-Beta4.0.0/var/master/servers/Web/config/config
 > 
 > my-user    20326 20232  0 17:54 ?        00:00:00 python
 > lib/python/omero/processor.py
 > --Ice.Config=/usr/local/omero-Beta4.0.0/var/master/servers/Processor0/config/config
 > 
 > my-user    20344 20325  0 17:54 ?        00:00:00 python manage.py
 > runserver --noreload
 > 
 > my-user    21775 20232  2 18:05 ?        00:00:00 python
 > lib/python/fsRunFSDropBox.py
 > --Ice.Config=/usr/local/omero-Beta4.0.0/var/master/servers/DropBox/config/config
 > 
 > 
 > fs.out:
 > 
 > 2009-04-07 18:00:08,519 INFO: fs.DropBox - Trying to start OMERO.fs
 > DropBox client
 > 2009-04-07 18:00:11,525 INFO: fs.DropBox - Failed to get session on
 > attempt 1
 > 2009-04-07 18:00:14,529 INFO: fs.DropBox - Failed to get session on
 > attempt 2
 > 2009-04-07 18:00:17,533 INFO: fs.DropBox - Failed to get session on
 > attempt 3
 > 2009-04-07 18:00:20,537 INFO: fs.DropBox - Failed to get session on
 > attempt 4
 > 2009-04-07 18:00:23,541 INFO: fs.DropBox - Failed to get session on
 > attempt 5
 > 2009-04-07 18:00:23,542 ERROR: fs.DropBox - Failed to get Session:
 > Traceback (most recent call last):
 >   File "/usr/local/omero-Beta4.0.0/lib/python/fsDropBox.py", line 40, in run
 >     sf = self.getOmeroServiceFactory()
 >   File "/usr/local/omero-Beta4.0.0/lib/python/fsDropBox.py", line 124,
 > in getOmeroServiceFactory
 >     raise Exception(excpt)
 > Exception: exception ::Ice::NoEndpointException
 > {
 >     proxy = BlitzManager -t @ BlitzAdapters
 > }
 > 2009-04-07 18:00:24,358 INFO: fs.DropBox - Trying to start OMERO.fs
 > DropBox client
 > 2009-04-07 18:00:27,361 INFO: fs.DropBox - Failed to get session on
 > attempt 1
 > .
 > .
 > 
 > 
 > master.err:
 > .
 > .
 >   File "/usr/lib64/python2.4/site-packages/Ice/Ice.py", line 766, in main
 >     status = self.run(args)
 >   File "/usr/local/omero-Beta4.0.0/lib/python/fsDropBox.py", line 40, in run
 >     sf = self.getOmeroServiceFactory()
 >   File "/usr/local/omero-Beta4.0.0/lib/python/fsDropBox.py", line 124,
 > in getOmeroServiceFactory
 >     raise Exception(excpt)
 > Exception: exception ::Ice::NoEndpointException
 > {
 >     proxy = BlitzManager -t @ BlitzAdapters
 > }
 > 
 > 
 > Blitz-o.log:
 > 
 > 2009-04-07 16:41:33,733 INFO  [                ome.services.blitz.Entry]
 > (      main) Creating OMERO.blitz. Please wait...
 > 2009-04-07 16:41:36,761 INFO  [ng.ShutdownSafeEhcacheManagerFactoryBean]
 > (      main) Initializing EHCache CacheManager
 > 2009-04-07 16:41:37,034 INFO  [ome.services.db.SelfCorrectingDataSource]
 > (      main) Found location in errorTimes: -1
 > 2009-04-07 16:41:37,035 INFO  [ome.services.db.SelfCorrectingDataSource]
 > (      main) Removing 0 from errorTimes
 > 2009-04-07 16:41:37,035 WARN  [ome.services.db.SelfCorrectingDataSource]
 > (      main) Registering error with list: Current size: 0
 > 2009-04-07 16:41:37,035 INFO  [ome.services.db.SelfCorrectingDataSource]
 > (      main) Sleeping for 0 then retry: 1
 > 2009-04-07 16:41:37,037 INFO  [ome.services.db.SelfCorrectingDataSource]
 > (      main) Found location in errorTimes: -1
 > 2009-04-07 16:41:37,037 INFO  [ome.services.db.SelfCorrectingDataSource]
 > (      main) Removing 0 from errorTimes
 > 2009-04-07 16:41:37,037 WARN  [ome.services.db.SelfCorrectingDataSource]
 > (      main) Registering error with list: Current size: 1
 > 2009-04-07 16:41:37,038 INFO  [ome.services.db.SelfCorrectingDataSource]
 > (      main) Sleeping for 1000 then retry: 2
 > 2009-04-07 16:41:38,044 INFO  [ome.services.db.SelfCorrectingDataSource]
 > (      main) Found location in errorTimes: -1
 > 2009-04-07 16:41:38,045 INFO  [ome.services.db.SelfCorrectingDataSource]
 > (      main) Removing 0 from errorTimes
 > 2009-04-07 16:41:38,045 WARN  [ome.services.db.SelfCorrectingDataSource]
 > (      main) Registering error with list: Current size: 2
 > 2009-04-07 16:41:38,046 ERROR [ome.services.db.SelfCorrectingDataSource]
 > (      main) Failed to acquire connection after retries=3
 > java.sql.SQLException: unable to get a connection from pool of a
 > PoolingDataSource containing an XAPool of resource
 > 6046fc17-e86a-4705-8b4a-1790059947ab with 0 connec
 > tion(s) (0 still available)
 >         at
 > bitronix.tm.resource.jdbc.PoolingDataSource.getConnection(PoolingDataSource.java:109)
 >         at
 > org.springframework.jdbc.datasource.DelegatingDataSource.getConnection(DelegatingDataSource.java:84)
 >         at
 > ome.services.db.SelfCorrectingDataSource.call(SelfCorrectingDataSource.java:102)
 >         at
 > ome.services.db.SelfCorrectingDataSource.callWithRetries(SelfCorrectingDataSource.java:75)
 >         at
 > ome.services.db.SelfCorrectingDataSource.getConnection(SelfCorrectingDataSource.java:59)
 >         at
 > org.springframework.jdbc.datasource.LazyConnectionDataSourceProxy.afterPropertiesSet(LazyConnectionDataSourceProxy.java:163)
 >         at
 > org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1368)
 >         at
 > org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1334)
 >         at
 > org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:473)
 >         at
 > org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory$1.run(AbstractAutowireCapableBeanFactory.java:409)
 >         at java.security.AccessController.doPrivileged(Native Method)