Installation fine, but can't get past login screens

[ncweiler]

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

[jmoore]

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

[ncweiler]

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?

[jmoore]

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

[ncweiler]

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!

[jmoore]

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

[ncweiler]

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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!

[ncweiler]

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

[ncweiler]

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


[ncweiler]

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!