Open Microscopy Environment

My Omero server installation seems to have gone fine, having followed the instructions at http://www.openmicroscopy.org/site/supp ... g-macports, but I can't get past the login screens either in omero.web or omero.insight. I've looked through the related topics on the board, but haven't found a solution that fixes my problem...

Here's me running and attempting to diagnose the server's issues:

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Wyrd:OMERO Nick$ bin/omero admin start
No descriptor given. Using etc/grid/default.xml
Waiting on startup. Use CTRL-C to exit
Wyrd:OMERO Nick$ bin/omero admin diagnostics

================================================================================
OMERO Diagnostics Beta4.2.2-r8718-Beta4.2-b56
================================================================================
       
Commands:   java -version                  1.6.0     (/usr/bin/java)
Commands:   python -V                      2.6.6     (/opt/local/bin/python -- 4 others)
Commands:   icegridnode --version          3.3.1     (/opt/local/bin/icegridnode)
Commands:   icegridadmin --version         3.3.1     (/opt/local/bin/icegridadmin)
Commands:   psql --version                 8.4.6     (/opt/local/lib/postgresql84/bin/psql)

Server:     icegridnode                    running
Server:     Blitz-0                        active (pid = 1086, enabled)
Server:     DropBox                        inactive (disabled)
Server:     FileServer                     active (pid = 1088, enabled)
Server:     Indexer-0                      active (pid = 1089, enabled)
Server:     MonitorServer                  inactive (disabled)
Server:     OMERO.Glacier2                 inactive (disabled)
Server:     OMERO.IceStorm                 inactive (disabled)
Server:     Processor-0                    active (pid = 1093, enabled)
Server:     Repository-1                   error: node `repo' couldn't be reached:
the node is not active
Server:     Tables-0                       inactive (disabled)
Server:     TestDropBox                    inactive (enabled)

Log dir:    /Applications/OMERO/var/log    exists

Log files:  Blitz-0.log                    119.0 KB      errors=2    warnings=95 
Log files:  DropBox.log                    3.0 KB        errors=6    warnings=0   
Log files:  FileServer.log                 0.0 KB       
Log files:  Indexer-0.log                  89.0 KB       errors=1    warnings=19 
Log files:  MonitorServer.log              2.0 KB        errors=3    warnings=0   
Log files:  OMEROweb.log                   9.0 KB        errors=29   warnings=0   
Log files:  Processor-0.log                3.0 KB       
Log files:  Tables-0.log                   n/a
Log files:  TestDropBox.log                n/a
Log files:  master.err                     4.0 KB       
Log files:  master.out                     0.0 KB       
Log files:  Total size                     0.23 MB

Parsing Blitz-0.log:[line:77] => Server restarted <=
Parsing Blitz-0.log:[line:689] => Server restarted <=
Parsing Blitz-0.log:[line:981] => Server restarted <=

Environment:OMERO_HOME=(unset)             
Environment:OMERO_NODE=(unset)             
Environment:OMERO_MASTER=(unset)           
Environment:PATH=/opt/local/lib/postgresql84/bin:/opt/local/bin:/opt/local/sbin:/usr/local/mysql/bin/:/Developer/usr/bin/:/opt/local/bin:/opt/local/sbin:/Library/Frameworks/Python.framework/Versions/3.1/bin:/Library/Frameworks/Python.framework/Versions/3.0/bin:/opt/local/bin:/opt/local/sbin:/Library/Frameworks/Python.framework/Versions/Current/bin:/opt/local/bin:/opt/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin
Environment:ICE_HOME=(unset)               
Environment:LD_LIBRARY_PATH=(unset)       
Environment:DYLD_LIBRARY_PATH=(unset)     

OMERO data dir: '/OMERO'   Exists? True   Is writable? True
OMERO.web status... DEVELOPMENT: You will have to check status by hand!


On Omero.insight I use the following settings after starting up the server in Terminal:
Username: root
Password: (password I set up in the db script step)
server: localhost
port: 4064 (default)

I get a Login Failure window with the error message: "Failed to log onto OMERO. Please check the port or try again later."

I set up omero.web to use the internal test server as described at http://www.openmicroscopy.org/site/supp ... stallation and get no errors when I run it:

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Wyrd:OMERO Nick$ bin/omero web start
Starting OMERO.web... Validating models...
0 errors found

Django version 1.1.1, using settings 'omeroweb.settings'
Development server is running at http://0.0.0.0:4080/
Quit the server with CONTROL-C.


But when I go to http://localhost:4080/webadmin/login/?url=/webadmin/ and enter the same username and password as above (running server omero:4064, SSL not checked), I get about five seconds during which Chrome is "waiting for localhost", and then the login page reloads with the following error: "Error: Server is not responding, please contact administrator." I have tried contacting myself, but I'm not sure what to tell me. The log in the Terminal after this action, by the way, reads:

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[17/Jan/2011 22:19:22] "GET /webadmin HTTP/1.1" 301 0
[17/Jan/2011 22:19:22] "GET /webadmin/ HTTP/1.1" 302 0
[17/Jan/2011 22:19:22] "GET /webadmin/login/?url=/webadmin/ HTTP/1.1" 200 1976
[17/Jan/2011 22:19:45] "POST /webadmin/login/ HTTP/1.1" 200 2153


Any guidance would be most helpful!

All the best,
Nick Weiler

---
Nicholas C. Weiler
Graduate Student in Neurosciences
Stephen J Smith Lab
Stanford University Medical Center
Beckman B139 - (510) 612 7423
nweiler@stanford.edu

The fact that Glacier2 and Storm are down points to your server not being fully configured:

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Server:     OMERO.Glacier2                 inactive (disabled)
Server:     OMERO.IceStorm                 inactive (disabled)


You most likely need to set DYLD_LIBRARY_PATH to your Ice install location, which is rather briefly described under "Environment variables" on the main installation page.

Cheers,
~Josh

OK, but which part of the installation do I need to rebuild after I change the path? I can't just re-run the install script, because some of the db tables already exist. Is there a good way to uninstall / remove the things I've installed & configured so far? Do I just need to uninstall postgres et al. and start over clean?

Hi Nick,

sorry for being unclear, but there's no problem with your installation, just with the environment that OMERO is running in. Something like the following should suffice:

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bin/omero admin stop
export DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:<your path to Ice's lib directory>
bin/omero admin start


You'll probably want to put that setting in your default environment by setting it in .bashrc or similar.

Cheers,
~Josh

OK - thanks for the clarification... Well, at any rate I have a brand new install of postgresql84 and postgresql84-erver, which I freshly set up according to the macports for OS 10.6 instructions (though I am running 10.5 - I've been attempting to cross-ref with the 10.5 installation instructions to make sure there are no inconsistencies). I've added the following line to my .profile:

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export DYLD_LIBRARY_PATH=/opt/local/var/macports/software/ice33-python25/3.3.1_0/opt/local/lib:$DYLD_LIBRARY_PATH


, but I still get the same problem in admin diagnostics:

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================================================================================
OMERO Diagnostics Beta4.2.2-r8718-Beta4.2-b56
================================================================================
       
Commands:   java -version                  1.5.0     (/usr/bin/java)
Commands:   python -V                      2.5.5     (/opt/local/bin/python -- 2 others)
Commands:   icegridnode --version          3.3.1     (/opt/local/bin/icegridnode)
Commands:   icegridadmin --version         3.3.1     (/opt/local/bin/icegridadmin)
Commands:   psql --version                 8.4.6     (/opt/local/lib/postgresql84/bin/psql)

Server:     icegridnode                    running
Server:     Blitz-0                        active (pid = 571, enabled)
Server:     DropBox                        inactive (disabled)
Server:     FileServer                     active (pid = 573, enabled)
Server:     Indexer-0                      active (pid = 574, enabled)
Server:     MonitorServer                  inactive (disabled)
Server:     OMERO.Glacier2                 inactive (disabled)
Server:     OMERO.IceStorm                 inactive (disabled)
Server:     Processor-0                    active (pid = 578, enabled)
Server:     Repository-1                   error: node `repo' couldn't be reached:
the node is not active
Server:     Tables-0                       inactive (disabled)
Server:     TestDropBox                    inactive (enabled)

Log dir:    /Applications/Omero/server/var/log exists

Log files:  Blitz-0.log                    26.0 KB       errors=0    warnings=12 
Log files:  DropBox.log                    1.0 KB        errors=2    warnings=0   
Log files:  FileServer.log                 0.0 KB       
Log files:  Indexer-0.log                  59.0 KB       errors=0    warnings=10 
Log files:  MonitorServer.log              0.0 KB        errors=1    warnings=0   
Log files:  OMEROweb.log                   0.0 KB       
Log files:  Processor-0.log                0.0 KB       
Log files:  Tables-0.log                   n/a
Log files:  TestDropBox.log                n/a
Log files:  master.err                     0.0 KB       
Log files:  master.out                     0.0 KB       
Log files:  Total size                     0.09 MB

Parsing Blitz-0.log:[line:76] => Server restarted <=

Environment:OMERO_HOME=(unset)             
Environment:OMERO_NODE=(unset)             
Environment:OMERO_MASTER=(unset)           
Environment:PATH=/opt/local/bin:/opt/local/sbin:/opt/local/lib/postgresql84/bin:/opt/local/bin:/opt/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin:/usr/local/git/bin
Environment:ICE_HOME=(unset)               
Environment:LD_LIBRARY_PATH=(unset)       
Environment:DYLD_LIBRARY_PATH=/opt/local/var/macports/software/ice33-python25/3.3.1_0/opt/local/lib:

OMERO data dir: '/OMERO'   Exists? True   Is writable? True
OMERO.web status... [NOT STARTED]


.

Should I be pointing directly at .../opt/local/lib within my ice33-python25 install, or should I just point to the install directory? I'll try a couple variations on this to see if it addresses the issue...

Thanks so much for your help working through this!

You'll need to point where the Ice*dylib libraries are. Can you try running glacier2router --version? Here's what I'm thinking is happening:

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$ glacier2router --version
3.3.1
$ echo $DYLD_LIBRARY_PATH
/opt/Ice-3.3.1-64/lib:/opt/Ice-3.3.1-64/python:
$ unset DYLD_LIBRARY_PATH
$ echo $DYLD_LIBRARY_PATH

$ glacier2router --version
dyld: Library not loaded: /opt/Ice-3.3/lib/libGlacier2.33.dylib
  Referenced from: /opt/Ice-3.3.1-64/bin/glacier2router
  Reason: image not found
Trace/BPT trap


Cheers,
~Josh

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================================================================================
OMERO Diagnostics Beta4.2.2-r8718-Beta4.2-b56
================================================================================
       
Commands:   java -version                  1.5.0     (/usr/bin/java)
Commands:   python -V                      2.5.5     (/opt/local/bin/python -- 2 others)
Commands:   icegridnode --version          3.3.1     (/opt/local/bin/icegridnode)
Commands:   icegridadmin --version         3.3.1     (/opt/local/bin/icegridadmin)
Commands:   psql --version                 8.4.6     (/opt/local/lib/postgresql84/bin/psql)

Server:     icegridnode                    running
Server:     Blitz-0                        active (pid = 867, enabled)
Server:     DropBox                        inactive (disabled)
Server:     FileServer                     active (pid = 869, enabled)
Server:     Indexer-0                      active (pid = 870, enabled)
Server:     MonitorServer                  inactive (disabled)
Server:     OMERO.Glacier2                 inactive (disabled)
Server:     OMERO.IceStorm                 inactive (disabled)
Server:     Processor-0                    active (pid = 874, enabled)
Server:     Repository-1                   error: node `repo' couldn't be reached:
the node is not active
Server:     Tables-0                       inactive (disabled)
Server:     TestDropBox                    inactive (enabled)

Log dir:    /Applications/Omero/server/var/log exists

Log files:  Blitz-0.log                    50.0 KB       errors=0    warnings=28 
Log files:  DropBox.log                    3.0 KB        errors=8    warnings=0   
Log files:  FileServer.log                 1.0 KB       
Log files:  Indexer-0.log                  63.0 KB       errors=0    warnings=19 
Log files:  MonitorServer.log              3.0 KB        errors=4    warnings=0   
Log files:  OMEROweb.log                   0.0 KB       
Log files:  Processor-0.log                39.0 KB       errors=10   warnings=71 
Log files:  Tables-0.log                   n/a
Log files:  TestDropBox.log                n/a
Log files:  master.err                     2.0 KB       
Log files:  master.out                     0.0 KB       
Log files:  Total size                     0.16 MB

Parsing Blitz-0.log:[line:76] => Server restarted <=
Parsing Blitz-0.log:[line:274] => Server restarted <=

Environment:OMERO_HOME=(unset)             
Environment:OMERO_NODE=(unset)             
Environment:OMERO_MASTER=(unset)           
Environment:PATH=/opt/local/bin:/opt/local/sbin:/opt/local/lib/postgresql84/bin:/opt/local/bin:/opt/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin:/usr/local/git/bin
Environment:ICE_HOME=(unset)               
Environment:LD_LIBRARY_PATH=(unset)       
Environment:DYLD_LIBRARY_PATH=/opt/local/var/macports/software/ice33-python25/3.3.1_0:/opt/local/var/macports/software/ice33-python25/3.3.1_0/opt/local/lib:

OMERO data dir: '/OMERO'   Exists? True   Is writable? True
OMERO.web status... [NOT STARTED]


OK, so this is still not working. Actually, it occurred to me that one obvious place where things may be messed up is in my Ice install: I got around the issues with Macports' ice-python26 versioning (http://www.openmicroscopy.org/site/supp ... g-macports) by macporting ice33-python25 instead (I don't know why I went with 2.5 - probably because that's used in the OS 10.5 instructions and I just followed along). This seemed to work to get me ice33 for python (and I believe it also installed ice33-cpp correctly, but I haven't tested it), but it may be treating Ice installation differently than the port recommended on your site...

Any thoughts? Thanks!

Sorry - didn't see your latest post. Will try that and get back to you! Thanks!

Hm - I get a different behavior:

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HR-sjsmith-1219793537:server Smithlab$ glacier2router --version
3.3.1
HR-sjsmith-1219793537:server Smithlab$ echo $DYLD_LIBRARY_PATH
/opt/local/var/macports/software/ice33-python25/3.3.1_0:/opt/local/var/macports/software/ice33-python25/3.3.1_0/opt/local/lib:
HR-sjsmith-1219793537:server Smithlab$ unset DYLD_LIBRARY_PATH
HR-sjsmith-1219793537:server Smithlab$ echo $DYLD_LIBRARY_PATH

HR-sjsmith-1219793537:server Smithlab$ glacier2router --version
3.3.1


Hi again. Success! I tracked down the Ice*.dylib files. MacPorts seemed to have put them in /opt/local/lib. However, adding this address causes the server startup to fail in the same way as described here: http://www.openmicroscopy.org/community/viewtopic.php?f=5&t=464&start=10

However, even when I make the suggested change to DYLD_LIBRARY_PATH:

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export DYLD_LIBRARY_PATH=/System/Library/Frameworks//ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Resources:/opt/local/lib


I got the same result: server start fails. Perhaps the code suggested at the above thread was just an example and I'm still missing the native java library that was already affected...

Anyway, I finally figured out (as I was about to copy & paste these libraries to a different folder and point the DYLD_LIBRARY_PATH at that), that the complete set of Ice dylib files was placed by Macports at /opt/local/var/macports/software/ice33-cpp/3.3.1_0/opt/local/lib, rather than in the .../ice33-py25/... folder I'd been looking in before. Many of the files are shortcuts to the files in opt/local/lib, but at any rate when I pointed the path to this folder, everything seems to work and I can get the web client up and running just fine.

Thanks for your help!