[ome-users] Unable to open Omero Insight/Importer
Paulo Almeida
palmeida at igc.gulbenkian.pt
Thu Nov 20 12:27:19 GMT 2008
Hi,
If possible, option 3 might be making the client use the same DNS as the
server. I don't know how it works with Java. Does it use something
like /etc/resolv.conf , or does it have its own DNS configuration?
- Paulo
On Thursday 20 November 2008 12:19, Chris Allan wrote:
> 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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