[ome-users] Unable to open Omero Insight/Importer
Nandakumar, Sriramkumar
sriramkumar at uky.edu
Wed Nov 19 21:32:19 GMT 2008
Hi Chris,
Thanks for the reply.
The root cause for this problem seems to be due to UnknownHostException.
It could not able to find myomero.uky.edu.
However I have specified this name under /etc/hosts
127.0.0.1 localhost
128.163.118.39 myomero.uky.edu myomero
I dont know why it is not recognizing still.
Is it due to network issue?
Please assist me in this regard.
Thanks in Advance.
Thanks & Regards,
Sriram.
________________________________________
From: Chris Allan [callan at blackcat.ca]
Sent: Wednesday, November 19, 2008 4:12 PM
To: Nandakumar, Sriramkumar
Cc: ome-users at lists.openmicroscopy.org.uk; jason at lifesci.dundee.ac.uk
Subject: Re: [ome-users] Unable to open Omero Insight/Importer
Hi Sriram,
Windows:
C:\Documents and Settings\<Username>\omero\log\omeroinsight.log
Mac OS X:
/Users/<Username>/omero/log/omeroinsight.log
Ciao.
-Chris
On 19 Nov 2008, at 19:40, Nandakumar, Sriramkumar wrote:
> Hi Chris and Jason,
>
> Thanks for the reply.
>
> 1) Please find my /etc/hosts configuration below,
>
> 127.0.0.1 localhost
> 128.163.118.39 myomero.uky.edu myomero
>
> where 128.163.118.39 is the IP Address, myomero.uky.edu is in the
> format hostname.network domain and myomero is the hostname
> which is similar as mentioned in the Omero trouble shooting page.
>
> 2) The /proc/sys/net/ipv4/tcp_window_scaling is set to 0.
>
> 3) The Ports 8080, 4444, 1098, 1099, 3873 were open.
>
> Am I missing anything other than this?
>
> I have went through the OmeroSecurity and OmeroTrouble shooting
> page, I couldn`t able to figure the exact solution for this problem.
> I have attached the outputs of netstat -na and ifconfig -a in
> this email for your reference.
>
> Furthermore it is not possible to me to get logs for both Omero
> Insight and Importer.
> I deployed OMERO.clients-Beta3.1.2 on windows. The log directory
> seems to be empty (c:\OMERO.clients-Beta3.1.2\log).
> Is there any other way to retrieve logs?
>
> I am seeing the following error message when Omero Server is
> running. Does it has any impact on the Omero clients?
>
> java.lang.IncompatibleClassChangeError
> at org.jnp.interfaces.NamingContext.lookup(NamingContext.java:
> 667)
> at org.jnp.interfaces.NamingContext.lookup(NamingContext.java:
> 774)
> at org.jnp.interfaces.NamingContext.lookup(NamingContext.java:
> 627)
> at javax.naming.InitialContext.lookup(InitialContext.java:392)
> at org.jboss.web.tomcat.security.SecurityFlushSessionListener.getSecurityManagerService
> (SecurityFlushSessionListener.java:201)
> at org.jboss.web.tomcat.security.SecurityFlushSessionListener.getSubjectAndSecurityDomain
> (SecurityFlushSessionListener.java:168)
> at org.jboss.web.tomcat.security.SecurityFlushSessionListener.sessionDestroyed
> (SecurityFlushSessionListener.java:81)
> at
> org
> .apache.catalina.session.StandardSession.expire(StandardSession.java:
> 702)
> at
> org
> .apache
> .catalina.session.StandardSession.isValid(StandardSession.java:592)
> at
> org
> .apache.catalina.session.ManagerBase.processExpires(ManagerBase.java:
> 681)
> at
> org
> .apache
> .catalina.session.ManagerBase.backgroundProcess(ManagerBase.java:666)
> at
> org
> .apache
> .catalina.core.ContainerBase.backgroundProcess(ContainerBase.java:
> 1315)
> at org.apache.catalina.core.ContainerBase
> $ContainerBackgroundProcessor.processChildren(ContainerBase.java:1600)
> at org.apache.catalina.core.ContainerBase
> $ContainerBackgroundProcessor.processChildren(ContainerBase.java:1609)
> at org.apache.catalina.core.ContainerBase
> $ContainerBackgroundProcessor.processChildren(ContainerBase.java:1609)
> at org.apache.catalina.core.ContainerBase
> $ContainerBackgroundProcessor.run(ContainerBase.java:1589)
> at java.lang.Thread.run(Thread.java:619)
> 2008-11-19 14:32:04,588 ERROR [Base.[jboss.web].[localhost].[/
> WebAdmin]] (boss.web]]) Session event listener threw exception
> java.lang.IncompatibleClassChangeError
> at org.jnp.interfaces.NamingContext.lookup(NamingContext.java:
> 667)
> at org.jnp.interfaces.NamingContext.lookup(NamingContext.java:
> 774)
> at org.jnp.interfaces.NamingContext.lookup(NamingContext.java:
> 627)
> at javax.naming.InitialContext.lookup(InitialContext.java:392)
> at org.jboss.web.tomcat.security.SecurityFlushSessionListener.getSecurityManagerService
> (SecurityFlushSessionListener.java:201)
> at org.jboss.web.tomcat.security.SecurityFlushSessionListener.getSubjectAndSecurityDomain
> (SecurityFlushSessionListener.java:168)
> at org.jboss.web.tomcat.security.SecurityFlushSessionListener.sessionDestroyed
> (SecurityFlushSessionListener.java:81)
> at
> org
> .apache.catalina.session.StandardSession.expire(StandardSession.java:
> 702)
> at
> org
> .apache
> .catalina.session.StandardSession.isValid(StandardSession.java:592)
> at
> org
> .apache.catalina.session.ManagerBase.processExpires(ManagerBase.java:
> 681)
> at
> org
> .apache
> .catalina.session.ManagerBase.backgroundProcess(ManagerBase.java:666)
> at
> org
> .apache
> .catalina.core.ContainerBase.backgroundProcess(ContainerBase.java:
> 1315)
> at org.apache.catalina.core.ContainerBase
> $ContainerBackgroundProcessor.processChildren(ContainerBase.java:1600)
> at org.apache.catalina.core.ContainerBase
> $ContainerBackgroundProcessor.processChildren(ContainerBase.java:1609)
> at org.apache.catalina.core.ContainerBase
> $ContainerBackgroundProcessor.processChildren(ContainerBase.java:1609)
> at org.apache.catalina.core.ContainerBase
> $ContainerBackgroundProcessor.run(ContainerBase.java:1589)
> at java.lang.Thread.run(Thread.java:619)
>
>
> It could be really helpful if you assist me in resolving this problem.
> I am Sorry if I am troubling you much.
>
> Thanks in Advance.
>
> Thanks & Regards,
> Sriram.
> ________________________________________
> From: Chris Allan [callan at blackcat.ca]
> Sent: Wednesday, November 19, 2008 10:39 AM
> To: Nandakumar, Sriramkumar
> Cc: ome-users at lists.openmicroscopy.org.uk
> Subject: Re: [ome-users] Unable to open Omero Insight/Importer
>
> HI Sriram,
>
> Yes, people have experienced this before. It's usually down to
> incorrectly configured name resolution and/or IP addresses.
>
> Please send us your omeroinsight.log from the "omero/log" directory
> on the system you're connecting from.
>
> Thanks for your feedback.
>
> -Chris
>
> On 18 Nov 2008, at 22:31, Nandakumar, Sriramkumar wrote:
>
>> Hi,
>> It is possible for me to open OMERO Insight and Importer in the
>> machine where I deployed OMERO Server.
>> It is not possible to open both Omero Insight and Importer in
>> another machines in the same LAN.
>> Has anyone experienced same kind of problem before?
>>
>> I could be really helpful if you can assist me in this problem
>>
>> Thanks in Advance.
>>
>> Thanks & Regards,
>> Sriram.
>> ________________________________________
>> From: Nandakumar, Sriramkumar
>> Sent: Monday, November 17, 2008 4:20 PM
>> To: josh.moore at gmx.de
>> Cc: ome-users at lists.openmicroscopy.org.uk
>> Subject: RE: [ome-users] Help Needed. Unable to open Omero Clients.
>>
>> Hi Josh,
>> Thanks for the reply.
>> Your suggestion was really very useful.
>> I have removed Icetea and deployed java seperately.
>> Now both Omero Insight and Import are opening on the machine where
>> I deployed Omero Server.
>> Now I want both these applications to be opened in another machines.
>> I have sent the output of netstat -na and ifconfig -a commands in
>> my previous mail.
>>
>> Could you please help me in resolving the OMERO Client problem?
>>
>> Once again Thanks a lot for your help.
>>
>>
>> Thanks & Regards,
>> Sriram.
>> ________________________________________
>> From: josh.moore at gmx.de [josh.moore at gmx.de]
>> Sent: Friday, November 14, 2008 4:38 PM
>> To: Nandakumar, Sriramkumar
>> Cc: ome-users at lists.openmicroscopy.org.uk
>> Subject: Re: [ome-users] Help Needed. Unable to open Omero Clients.
>>
>> Nandakumar, Sriramkumar writes:
>>> Hi Josh,
>>> I forgot to mention my OS details in my previous mail.
>>> I am using Fedora 8 and my Java version is 1.6.
>>
>> Thanks for this. And which Java distribution are you using?
>>
>> java -version
>>
>> A similar exception as in your log can also be seen here:
>>
>> http://markmail.org/message/i3v7a63wpfggiwl7
>>
>> due to using IceTea. If that is the case, could you install the
>> Java SDK
>> from Sun and try again; if not, we'll dig a little deeper.
>>
>> Best wishes,
>> ~Josh.
>>
>>
>>> Thanks & Regards,
>>> Sriram.
>>> ________________________________________
>>> From: Nandakumar, Sriramkumar
>>> Sent: Friday, November 14, 2008 3:05 PM
>>> To: josh.moore at gmx.de
>>> Cc: ome-users at lists.openmicroscopy.org.uk
>>> Subject: RE: [ome-users] Help Needed. Unable to open Omero Clients.
>>>
>>> Hi Josh,
>>>
>>> Thanks for the reply.
>>>
>>> I have attached the outputs of netstat -na and ifconfig -a in
>>> this mail for your reference.
>>> In my previous mail I have mentioned that it is not possible for
>>> me to invoke Omero Insight even the machine where I have deployed
>>> Omero Server.
>>> In the Omero Insight log I saw Null pointer exception in the
>>> beginning itself. I suspect that may be the reason why Insight is
>>> not invoked.
>>> I have attached the logs of Omero Insight in this mail.
>>>
>>> It would be really helpful if you can assist me in resolving this
>>> Omero Client problem.
>>>
>>> Thanks in Advance.
>>>
>>> Thanks & Regards,
>>> Sriram.
>>> ________________________________________
>>> From: josh.moore at gmx.de [josh.moore at gmx.de]
>>> Sent: Friday, November 14, 2008 3:25 AM
>>> To: Nandakumar, Sriramkumar
>>> Cc: ome-users at lists.openmicroscopy.org.uk
>>> Subject: [ome-users] Help Needed. Unable to open Omero Clients.
>>>
>>> Nandakumar, Sriramkumar writes:
>>>> Hi,
>>>
>>> Hello Sriramkumar,
>>>
>>>> These are the messages displayed when starting the Omero server. I
>>>> am seeing two STDERR messages (last two lines) and I am not sure
>>>> about this error. But it is possible for me to see the Omero
>>>> server page in the screen without any problem. ...
>>>
>>>> 2008-11-13 16:21:42,504 ERROR [ STDERR] ( main) Nov 13, 2008
>>>> 4:21:42 PM java.util.prefs.FileSystemPreferences$7 run WARNING:
>>>> Prefs file removed in background /root/.java/.userPrefs/prefs.xml
>>>> 2008-11-13 16:21:42,506 ERROR [ STDERR] ( main) Nov 13, 2008
>>>> 4:21:42 PM java.util.prefs.FileSystemPreferences$7 run WARNING:
>>>> Prefs file removed in background
>>>> /usr/lib/jvm/java-1.7.0-icedtea-1.7.0.0/jre/.systemPrefs/prefs.xml
>>>
>>> These two "errors" come straight from Java and unfortunately, or
>>> fortunately depending on how you look at it, have nothing to do with
>>> OMERO. You can safely ignore them, but if you are interested you
>>> might
>>> look at:
>>>
>>> http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=4751177
>>>
>>> for the original bug report. They are related to how Java is
>>> installed
>>> on Linux.
>>>
>>>> 1) All the necessary ports such as 8080, 1098, 4444, 3873, 1099
>>>> are open
>>>> 2) Please find my /etc/hosts
>>>>
>>>> 127.0.0.1 localhost
>>>> 128.163.118.171 myomero.uky.edu myomero
>>>>
>>>> where myomero is my hostname and myomero.uky.edu is in the format
>>>> (hostname.network domain)
>>>>
>>>> which is as mentioned in the Omero troubleshooting page.
>>>
>>> If you can reach the server locally with insight and importer, but
>>> not
>>> from another machine, then unless I'm mistaken this must be a
>>> networking issue. Could you send us the full output of:
>>>
>>> netstat -na
>>> ifconfig -a
>>>
>>> and perhaps a little information about your operating system. All of
>>> this can be done off list if you prefer.
>>>
>>> Best wishes,
>>> ~Josh.
>> _______________________________________________
>> ome-users mailing list
>> ome-users at lists.openmicroscopy.org.uk
>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
> <ifconfig.txt><netstat.txt>
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