[ome-users] Omero Beta 4 installation problems
Chris Roome
Chris.Roome at mpimf-heidelberg.mpg.de
Wed Apr 8 08:56:15 BST 2009
Hi all,
I would be very grateful for any help with my attempts to install Omera
4 please! Sorry for the long e-mail.
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.
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
Usage: icegridadmin [options]
Options:
-h, --help Show this message.
-v, --version Display the Ice version.
etc. etc.
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
>>>
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").
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.
Any help or info would be very much appreciated!
Many thanks & regards,
Chris.
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)
.
.
.
.
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