[ome-users] Able to Open Omero Clients now. Problem resolved.
Nandakumar, Sriramkumar
sriramkumar at uky.edu
Thu Nov 20 18:48:50 GMT 2008
Hi Chris,
I have manually configured DNS for the IP address using our network administrator and it is now possible to invoke both Omero Importer and Insight
without any issues.
I would like to specially thank you, Jason and Josh for helping me out in resolving this problem.
Based on my experience on OMERO 3.1.1, I would like to provide the following feedbacks,
1) For Fedora 8, we have not manually install Java SDK, because it contains IceTea which is not compatible for Omero.
2) In order to make specific ports open such as 8080, 4444, 3873, 1098, 1099, we can use a tool called firestarter which helps to select specific ports, so we dont need to use the following options at all,
iptables -P INPUT drop
iptables -A INPUT -p tcp --dport 1098 -j ACCEPT
iptables -A INPUT -p tcp --dport 1099 -j ACCEPT
iptables -A INPUT -p tcp --dport 4444 -j ACCEPT
iptables -A INPUT -p tcp --dport 3873 -j ACCEPT
3) It is always better to map the DNS with the IP address using the network administrator manually rather than specifying it in /etc/hosts.
Once again I would like to thank the developers in helping me for deploying OMERO.
Thanks & Regards,
Sriram.
________________________________________
From: Chris Allan [callan at blackcat.ca]
Sent: Thursday, November 20, 2008 7:19 AM
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,
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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