[ome-users] OMERO.web install under Mac OS X 10.6 - got a new problem
Josh Moore
josh.moore at gmx.de
Fri Jun 11 08:14:56 BST 2010
On 6/10/10 11:52 PM, Taylor, Ronald C wrote:
>
> Hi folks,
>
Hi Ron,
> After I set some values with
> omero web settings
>
> to use OMERO.web at localhost:8000
>
> something went wrong, and now I can't bring up the Omero server at all. Darn - thought I was up and running - but not yet. I did not see any error messages when I executed "omero web settings", so don't know why I'm having problems now.
>
> So - I start Postgres, and it runs OK (I check with "pg_ctl status").
>
> I then try
>
> omero admin start
>
> I don't get any on-screen error msgs, but the startup process times out after five minutes.
>
The failure after 5 minutes means that the central server didn't come
up, but the manager (icegridnode) is still running. You'd need to enter
bin/omero admin stop to shut everything down.
> The second time I try "omero admin start", I get an one-line onscreen msg saying
> Icegridnode: failure occurred in daemon
>
This is expected in 4.1 unless you shutdown completely.
> And there is a one line entry in
> /Library/Omero/Versions/4.1.1/omero_dist/lob/master.err
>
> Saying that there is an icegridnode error: an IceGrid registry is already running and listening on client endpoints 'tcp -h 127.0.0.1 -p 4061'
>
>
> I have attached all the log files that I get after I did another shutdown of my Mac, started Postgres again, and then attempt a
> omero admin start
>
> As before, I simply get a time out msg after 5 minutes, with no error msg to the command prompt window.
>
> I have also attached my .bash_profile file, in case I did something wrong there.
>
> Any help would be much appreciated, as always.
>
None of your Java servers started. Looking in master.out,
Error occurred during initialization of VM
Error occurred during initialization of VM
Unable to load native library: libjava.jnilib
Unable to load native library: libjava.jnilib
one of the recent changes to your environment has broken your Java
install. Do you have any idea what that change may have been?
~J.
> Ron
>
> ___________________________________________
> Ronald Taylor, Ph.D.
> Computational Biology& Bioinformatics Group
> Pacific Northwest National Laboratory
> 902 Battelle Boulevard
> P.O. Box 999, Mail Stop J4-33
> Richland, WA 99352 USA
> Office: 509-372-6568
> Email: ronald.taylor at pnl.gov
>
> -----Original Message-----
> From: Will Moore [mailto:will at lifesci.dundee.ac.uk]
> Sent: Thursday, June 10, 2010 12:31 PM
> To: Taylor, Ronald C
> Cc: 'ome-users at lists.openmicroscopy.org.uk'; 'Arcieri, Kenneth (NIH/NICHD) [V]'
> Subject: Re: [ome-users] OMERO.web install under Mac OS X 10.6 on a MacBook isolated from the net
>
> Hi Ron,
>
> Yes, you are exactly right.
> localhost:8000
>
> The other settings don't really matter. You can make up any invalid values here if you don't actually want the webclient to try and send mail for you.
>
> And then connect to
> localhost:8000/webadmin or ocalhost:8000/webclient
>
> Good luck,
>
> Will.
>
>
> On 10 Jun 2010, at 19:37, Taylor, Ronald C wrote:
>
>
>> Hello Will, Ken, all,
>>
>> Hopefully a simple question to answer:
>>
>> How do I set up the OMERO.web server to be used on my MacBook when my
>> MacBook is not on the network? That is, since I have a personal
>> MacBook that I am not allowed to put on our intranet, and I want to
>> try out the OMERO.web web interface on it, can I set the default
>> Django server to function with my MacBook serving as a "localhost"?
>>
>> Specifically, I want to find out how to I answer the questions in
>>
>> ../bin/omero web settings
>>
>> Would the domain be
>> localhost:8000 ?
>>
>> How do I answer the questions on email address and SMTP server host,
>> and on SMTP server port and SMTP server username?
>>
>>
>> I presume that there are some settings for such a localhost that will
>> still allow me to bring up the web server via
>>
>> omero admin ice
>> And then use
>> server enable Web
>> server start Web
>>
>> And then connect to the server's home page in my Firefox browser at,
>> say, localhost:8000
>>
>> Is this doable?
>>
>> Ron
>> ___________________________________________
>> Ronald Taylor, Ph.D.
>> Computational Biology& Bioinformatics Group Pacific Northwest
>> National Laboratory
>> 902 Battelle Boulevard
>> P.O. Box 999, Mail Stop J4-33
>> Richland, WA 99352 USA
>> Office: 509-372-6568
>> Email: ronald.taylor at pnl.gov
>>
>>
>> -----Original Message-----
>> From: Taylor, Ronald C
>> Sent: Tuesday, June 08, 2010 11:03 AM
>> To: 'Will Moore'
>> Cc: ome-users at lists.openmicroscopy.org.uk; Swan, Jeremy (NIH/NICHD)
>> [C]; Ronald Taylor
>> Subject: RE: [ome-users] OMERO client install attempt under Mac OS X
>> 10.6 - the client login popup
>>
>>
>> Will,
>>
>> Yea! Those settings worked. Finally up and running, at least on my
>> Mac. Thank you very much. Just tried the Insight and Importer and I
>> could get into both using the settings you suggested.
>>
>> So - I'll start to play around with some image files. And finish the
>> install, adding OMERO.web using Ken's manual as a guide.
>>
>> Again, thanks much.
>> Ron
>>
>> -----Original Message-----
>> From: Will Moore [mailto:will at lifesci.dundee.ac.uk]
>> Sent: Tuesday, June 08, 2010 12:54 AM
>> To: Taylor, Ronald C
>> Cc: ome-users at lists.openmicroscopy.org.uk; Swan, Jeremy (NIH/NICHD)
>> [C]; Ronald Taylor
>> Subject: Re: [ome-users] OMERO client install attempt under Mac OS X
>> 10.6 - would appreciate some help on the client login popup
>>
>>
>> Hi Ronald,
>>
>> Have you tried:
>>
>> localhost (port 4063)
>> user: root
>> password: omero
>>
>> Unless I'm missing something, that should work for you?
>>
>> Will.
>>
>> On 7 Jun 2010, at 22:37, Taylor, Ronald C wrote:
>>
>>
>>> Just in case anybody was wondering: I did try "127.0.0.1" for the
>>> server address (and left the port at the default of 4063). Did not
>>> work - at least, not combined with a Username of "omero" and Password
>>> of "omero".
>>> Ron
>>>
>>> -----Original Message-----
>>> From: Taylor, Ronald C
>>> Sent: Monday, June 07, 2010 2:26 PM
>>> To: 'Arcieri, Kenneth (NIH/NICHD) [V]';
>>> ome-users at lists.openmicroscopy.org.uk
>>> ; 'callan at lifesci.dundee.ac.uk'; Swan, Jeremy (NIH/NICHD) [C]
>>> Cc: Taylor, Ronald C; 'Ronald Taylor'
>>> Subject: OMERO client install attempt under Mac OS X 10.6 - would
>>> appreciate some help on the client login popup
>>>
>>>
>>> Ken, Jeremy, other OMERO users,
>>>
>>> I think I am very close to getting (finally) OMERO running on at
>>> least one machine. I have been following Ken's Mac 10.6 install
>>> manual, except instead of creating a separate omero account I have
>>> been doing the install in my pre-existing "RT" account.
>>>
>>> This is being done on my own personal Mac, just upgraded to 10.6.
>>> (Waiting on a OS 10.6 upgrade to a larger Mac server in our lab.)
>>>
>>> I have apparently installed everything for the OMERO server correctly
>>> this time. I do an
>>>
>>> omero admin start
>>> And
>>> omero admin diagnostics
>>>
>>> And the diagnostics appear OK, from what I can gather.
>>>
>>> However, I cannot bring up the client successfully. I have not yet
>>> installed the OMERO web server - from what I understand, that is not
>>> required to get a client connection on the same machine, and the
>>> server-client combination is the thing I want to test as fast as
>>> possible. Do I have that correct - I can use the client before
>>> installing the web server?
>>>
>>> Presuming I could manage without the web server for my test, I went
>>> ahead and installed the OMERO client zip file OMERO.clients-
>>> Beta4.1.1.mac.zip, which matches the server release.
>>>
>>> I then double-clicked on the OMERO.insight icon in the client
>>> directory. Got the popup. This is where my current problem is.
>>>
>>> When I earlier installed the server and ran bin/omero db script
>>>
>>> I gave the server the root password of "omero". Also, the omero
>>> Postgres account was named "omero" and has the password "omero". All
>>> this is being done in my Mac OS account of "RT".
>>>
>>> My problem now is I can't get past the popup. I enter "omero" for the
>>> Username and "omero" for the Password. Is that the correct thing to
>>> do? Does my OS account of "RT" come into play here in any way?
>>>
>>> Also - the client popup window says that I need to "Add a new
>>> server".
>>> Don't know what this means. When I click on that option I get an
>>> empty text box, followed by something for a port that defaults to
>>> "4063".
>>> Have no idea how to fill this out.
>>>
>>> As I write this, my MacBook is not connected to the net - personal
>>> machines are not allowed on the lab intranet. So - it does not any IP
>>> address to put in. I tried entering "localhost", but that did not
>>> work.
>>>
>>> What server is this entry panel referring to - the server started by
>>> "omero admin start"? Does that come up by default on port 4063? Or
>>> does this refer the OMERO web server, which I have not set up yet?
>>> Do I need to set up the web server before getting the client app to
>>> work?
>>>
>>> I checked they OMERO clients User Guide. Sadly, cannot find anything
>>> useful on how to fill out the initial log in screen! In sect 2.2 it
>>> says
>>>
>>> "When you start OMERO.importer, you will be asked to log in (See
>>> Figure 2.2-1). The administrator who set up OMERO can provide you
>>> with a user account and the address of the OMERO.server where your
>>> images will be stored.
>>> You provide the address of the OMERO server by selecting the button
>>> and entering the details in the form provided."
>>>
>>> Well - duh. Unforunately, I'm the admin and I don't know how to
>>> provide myself with the correct account name and server address to
>>> use.
>>>
>>> Would very much appreciate some help - hopefully OMERO users (who
>>> have logged in!) can answer these questions in just a couple
>>> sentences.
>>>
>>> - Ron
>>>
>>>
> William Moore
> Wellcome Trust Centre for Gene Regulation& Expression College of Life Sciences MSI/WTB/JBC Complex University of Dundee Dow Street Dundee DD1 5EH United Kingdom
>
> Phone 01382 386364
> http://openmicroscopy.org.uk
>
>
>
>
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>
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