[ome-users] Unable to open Omero Insight/Importer
Chris Allan
callan at blackcat.ca
Thu Nov 20 12:19:55 GMT 2008
Hi Sriram,
The server is sending that hostname to the client and the client
cannot resolve it. That's the problem.
Option 1: Put myomero.uky.edu in DNS at your site (tricky and unlikely)
Option 2: Delete the "128.163.118.39 myomero.uky.edu myomero" line
from your /etc/hosts file
Let us know if the second option doesn't work.
Ciao.
-Chris
On 19 Nov 2008, at 21:32, Nandakumar, Sriramkumar wrote:
> 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.getSecurit
>> yManagerService
>> (SecurityFlushSessionListener.java:201)
>> at
>> org.jboss.web.tomcat.security.SecurityFlushSessionListener.getSubject
>> AndSecurityDomain
>> (SecurityFlushSessionListener.java:168)
>> at
>> org.jboss.web.tomcat.security.SecurityFlushSessionListener.sessionDes
>> troyed
>> (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.getSecurit
>> yManagerService
>> (SecurityFlushSessionListener.java:201)
>> at
>> org.jboss.web.tomcat.security.SecurityFlushSessionListener.getSubject
>> AndSecurityDomain
>> (SecurityFlushSessionListener.java:168)
>> at
>> org.jboss.web.tomcat.security.SecurityFlushSessionListener.sessionDes
>> troyed
>> (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>
>
> <importer.log><omeroinsight.log><omeroinsight.log.1>
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