[ome-users] - install on Red Hat Linux desktop - question on install of ICE 3.3.1
Taylor, Ronald C
ronald.taylor at pnl.gov
Tue Jun 8 20:56:18 BST 2010
Ken,
Guess this is my lucky day - I just got the Linux version up and running, in addition to the copy of OMERO on my MacBook.
Turns out that there was a problem with the Postgres postmaster.pid file. Deleted it, did a hard reboot, restarted Postgres and the OMERO server, and everything now runs fine using ICE 3.3.1. I can get into the Insight and Importer clients, and I've been able to start the OMERO WEB server via ICE, and access the admin and user web pages, again being able to login to them OK.
So - I think I can start playing around with some images. Thanks for all the help.
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: Arcieri, Kenneth (NIH/NICHD) [V] [mailto:kenneth.arcieri at nih.gov]
Sent: Tuesday, June 08, 2010 6:00 AM
To: Taylor, Ronald C; 'Chris Allan'; 'ome-users at lists.openmicroscopy.org.uk'
Cc: 'josh at glencoesoftware.com'; Ronald Taylor
Subject: RE: [ome-users] - install on Red Hat Linux desktop - question on install of ICE 3.3.1 - I appear to have regressed and now can't invoke the server
Can you attach the log files from your server's log directory and send them to us/me? It would be a lot easier to debug this problem with them.
Thanks,
-Ken
-----Original Message-----
From: Taylor, Ronald C [mailto:ronald.taylor at pnl.gov]
Sent: Monday, June 07, 2010 8:22 PM
To: 'Chris Allan'; 'ome-users at lists.openmicroscopy.org.uk'
Cc: 'josh at glencoesoftware.com'; Ronald Taylor; Taylor, Ronald C; Arcieri, Kenneth (NIH/NICHD) [V]
Subject: RE: [ome-users] - install on Red Hat Linux desktop - question on install of ICE 3.3.1 - I appear to have regressed and now can't invoke the server
Hello Chris and other OMERO developers and users,
In addition to my attempt to install OMERO on my MacBook (described in a separate email sent earlier today), I am continuing to try to install OMERO on my Red Hat Linux desktop. I've been told to backtrack to using ICE 3.3.1, rather than the ver 3.4.0 that I had installed (see emails at bottom).
So - I just tried this. Unfortunately, I still need help.
Here's what happened:
1) using Ken Arcieri's instructions for doing an ICE 3.3.1 install (shown on pp 6-7 of his Mac OS install manual) as a template (those being the most detailed instructions that I could find), I deleted the 3.4.0 rel and reinstalled ICE using 3.3.1 into
/sid/Omero/Ice/Ice-3.3.1
on my Linux desktop, sidney.pnl.gov.
As best I as can determine from the "make" screen output, things went OK.
I changed my .mycshrc file to use 3.3.1 in four places:
I added /sid/Omero/Ice/Ice-3.3.1/bin to PATH I added /sid/Omero/Ice/Ice-3.3.1/lib to LD_LIBRARY_PATH I added /sid/Omero/Ice/Ice-3.3.1/python to PYTHONPATH I set ICE_HOME to /sid/Omero/Ice/Ice-3.3.1
I did not alter anything else in .mycshrc.
I did not alter anything else in the Omero set of directories - that is, I only re-installed the Ice code. With one exception: I had to install an RPM that contained "db.jar" for the BerkeleyDB. Apparently the RPM that was installed previously on sidney for the basic BerkeleyDB package lacked the java parts. Don't know why this this lack did not produce errors the earlier Ice 3.4.0 install, but the previously missing "db.jar" is now in /usr/share/java/db.jar and the "make install" in the Ice subdir ./java appeared to run OK today.
I rebooted sidney.
I then tried to invoke the server:
sidney26% omero admin start
No descriptor given. Using etc/grid/default.xml
icegridnode: failure occurred in daemon
sidney27%
So - something is going wrong, involving icegridnode. Any suggestions as to what to try?
Do I need to reinstall anything else now that I've changed the release of Ice? Is there something I need to add to CLASSPATH in my .mycshrc file? Do any of the *.jar files in the ../omero_dist/lib/server directory have to be manually added to the CLASSPATH?
One minor note: the versions of the jgoodies.forms and jgoodies.looks that I downloaded and used in the java part of the ICE install are
forms-1.3.0.jar
looks-2.3.1.jar
Those *.jar files are the files I named in
/sid/Omero/Ice_install/Ice-3.3.1/java/config/build_properties for the "make" run
As in the continuing saga of my Mac install, any help for this Linux install would be much appreciated.
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: Thursday, June 03, 2010 12:43 PM
To: 'Chris Allan'
Cc: 'josh at glencoesoftware.com'; 'ome-users at lists.openmicroscopy.org.uk'; Ronald Taylor; Taylor, Ronald C
Subject: RE: [ome-users] Newbie question - cannot get Omero client up - won't accept userid and password
Chris,
OK - I will backtrack to using the earlier version of ICE for my install under Linux.
Ron
-----Original Message-----
From: Chris Allan [mailto:callan at lifesci.dundee.ac.uk]
Sent: Thursday, June 03, 2010 12:43 AM
To: Taylor, Ronald C
Cc: 'josh at glencoesoftware.com'; 'ome-users at lists.openmicroscopy.org.uk'; Ronald Taylor
Subject: Re: [ome-users] Newbie question - cannot get Omero client up - won't accept userid and password
On 26 May 2010, at 01:36, Taylor, Ronald C wrote:
>
> Hello Josh and the list,
Hi Ron.
>
> Sorry for the delay in reply - had to go to a workshop and then switch to another project for several days. So, in answer to Josh's questions as to my nonfunctioning OMERO install, I have attached:
>
> 1) the omeroinsight.log file
> from ~rtaylor/omero/log
There isn't a connection here but I don't think that really has much to do with your connectivity problems.
>
> I was indeed able to find this file, now that I understood where to look.
>
> 2) the Blitz-0.log file
> from where I installed OMERO, in
> /sid/Omero/Omero_install/omero_dist/var/log
The server appears to have started up correctly so I don't see a problem there.
>
> 3) a record file showing all the screen output when I start OMERO, run diagnostics, and stop it. This record shows the onscreen results as of today.
>
> I still have not changed my version of ICE. I believe that the advice is to go back to ICS 3.3.1 rather than the 3.4.0 version I currently am using. I plan to try that tomorrow, before leaving on a trip. However, if Josh and anybody else who has a moment could check the log files and see if the contents indicate that the problem is indeed the version of ICE used - or if the problem may be something else, I would very much appreciate it.
That's definitely the first place to start. ICE 3.4.0 is not going to work with the clients at all.
> - Ron
-Chris
>
> ___________________________________________
> 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: Josh Moore [mailto:josh at glencoesoftware.com]
> Sent: Friday, May 14, 2010 12:10 PM
> To: Taylor, Ronald C
> Cc: ome-users at lists.openmicroscopy.org.uk
> Subject: Newbie question - cannot get Omero client up - won't accept
> userid and password - files to view
>
> Forwarding to the list.
>
> Taylor, Ronald C writes:
>>
>> Josh,
>>
>> I don't have an ~omero directory. I did the entire install as > myself, as user "rtaylor".
>
> Sorry. I meant a directory "omero" in your home directory.
>
>> In any event, I cannot find a omeroinsight.log file. Maybe it never > gets created, since the *.sh command I invoke to bring up the Java > client never gets past the userid/pwd login popup?
>
> The login talks to the server, so if there was a version issue with Ice that would explain it. Does anything get printed to the console?
>
> ~J
>
>> I have attached all the log files that I could find under >
>> /sid/Omero/Omero_install/omero_dist/var/log
>>
>> I have also attached a file with the screen output I got when > setting the Omero root user password to r*****9. Looks like it > worked OK, from the screen output.
>>
>> So - I try to invoke the client using OMEROinsight_unix.sh
>>
>> and these combinations of uerid/pwd do not work in the popup:
>>
>> rtaylor/r*****9
>>
>> omero/r*****9
>>
>> omero/omero
>>
>> Still stuck. Very happy to get some help! BTW - the PostgreSQL > install appeared to work fine, with an "omero" user with password > "omero" set up to own an "omero" db.
>>
>> Ron
>
> -----Original Message-----
> From: Josh Moore [mailto:josh at glencoesoftware.com]
> Sent: Wednesday, May 12, 2010 12:01 AM
> To: Taylor, Ronald C
> Cc: 'ome-users at lists.openmicroscopy.org.uk'
> Subject: Re: [ome-users] Newbie question - cannot get Omero client up
> - won't accept userid and password
>
>
> Could you possibly send the logs for Insight
> (~/omero/log/omeroinsight.log) and the main server log
> (var/log/Blitz-0.log) ? This may be an issue with your using a newer version of Ice:
>
>> Commands: icegridnode --version 3.4.0 (/sid/Omero/Ice/Ice-3.4.0/bin/icegridnode)
>
> We currently deploy with 3.3.1.
>
> Cheers,
> ~Josh.
>
>
>>
>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>>
>> Hello folks,
>>
>> I'm a newcomer. I've just installed Omero on my Red Hat Linux desktop and am now trying to star tup the Omero Java client. However, the opening box in the client asks for userID and password and won't accept what I've tried. So - I'm stuck.
>>
>> I set the root user password like so:
>>
>> /sid/Omero/Omero_install/omero_dist
>> sidney193%
>>
>> sidney193% bin/omero db script
>>
>> Please enter omero.db.version [OMERO4.1]:
>> Please enter omero.db.patch [0]:
>> Please enter password for OMERO root user: r*****9 > > Please
>> re-enter password for OMERO root user: r*****9 > > Saving to
>> /sid/Omero/Omero_install/omero_dist/OMERO4.1__0.sql
>> sidney194%
>>
>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>>
>> Omero is up, as can be seen from the diagnostics:
>>
>> sidney87% omero admin diagnostics
>>
>> =====================================================================
>> =========== OMERO Diagnostics Beta-4.1.1-r5927-b91 >
>> =====================================================================
>> ===========
>>
>> Commands: java -version 1.6.0 (/msrc/apps/jdk_1.6/bin/java -- 2 others)
>> Commands: python -V 2.6.5 (/sid/Omero/Python/bin/python -- 2 others)
>> Commands: icegridnode --version 3.4.0 (/sid/Omero/Ice/Ice-3.4.0/bin/icegridnode)
>> Commands: icegridadmin --version 3.4.0 (/sid/Omero/Ice/Ice-3.4.0/bin/icegridadmin)
>> Commands: psql --version 8.3.10 (/sid/Omero/Postgres/8.3/bin/psql)
>>
>> Server: icegridnode running
>> Server: Blitz-0 active (pid = 7016, enabled)
>> Server: DropBox inactive (disabled)
>> Server: FSServer active (pid = 7029, enabled)
>> Server: Indexer-0 active (pid = 7031, enabled)
>> Server: OMERO.Glacier2 active (pid = 7034, enabled)
>> Server: OMERO.IceStorm inactive (disabled)
>> Server: Processor-0 inactive (disabled)
>> Server: Tables-0 inactive (disabled)
>> Server: TestDropBox inactive (enabled)
>> Server: Web active (pid = 7774, enabled)
>>
>> Log dir: /sid/Omero/Omero_install/omero_dist/var/log exists
>>
>> Log files: Blitz-0.log 44.0 KB errors=2 warnings=34
>> Log files: DropBox.log n/a
>> Log files: FSServer.log 2.0 KB errors=0 warnings=12
>> Log files: Indexer-0.log 3.0 KB errors=0 warnings=2
>> Log files: OMEROweb.log 0.0 KB
>> Log files: OMEROweb.log.2010-05-11 0.0 KB
>> Log files: Processor-0.log n/a
>> Log files: Tables-0.log n/a
>> Log files: TestDropBox.log n/a
>> Log files: master.err 6.0 KB errors=0 warnings=4
>> Log files: master.out 0.0 KB
>> Log files: Total size 0.06 MB
>> sidney88%
>>
>>
>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>>
>> But when I invoke the java client using > > OMEROinsight_unix.sh
>> <ret> (client version is Beta4.1.1.linux.) > a popup window comes up that asks for userid and password.
>>
>> I have tried both
>> omero / r*****9
>> And
>> root / r*****9
>>
>> Niether worked. So - I'm stumped. Would very much appreciate help.
>>
>> - Ron Taylor
> <omeroinsight.log><record_of_omero_startup_5_25_10><Blitz-0.log>______
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