Open Microscopy Environment

I think I finally have OMERO set up and configured on OS X 10.6.2 using mod_WSGI.

I'm using the built-in Apache 2.2.13
MacPorts Python 2.6.5, postgreSQL 8.3, Ice 3.3.1
pil, matplot & numPy all from MacPorts

I can connect to the device from remote machines using Firefox and I get the OMERO.webadmin 'page', but when I attempt to log in as 'root' using the password I created when running the db script, I get: "Error: Client version does not match server, please contact administrator" blazened above the username and password fields. I'm very sure I'm entering the root password correctly. I fact, I've re-set it a couple of times just to be sure

Is this possibly due to the OMERO's insistence on using port 4064? And if so, how to I rectify the situation?

Also, I understand that even with SSL deselected in the login screen, the username and password are still encrypted. Is there something I need to configure in Apache to accommodate this? (I have no SSL certificate for this host).

I'm appending my OMERO diagnostics output at the bottom of this post.

Also, here's a snippet from the OMEROweb.log that corresponds to my connection and attempted login:

******************** OMEROweb.log **********************

Thu, 02 Sep 2010 18:54:31 views-web INFO INIT '19722'
Thu, 02 Sep 2010 20:44:36 views-feedback ERROR handler404: Page not found
Thu, 02 Sep 2010 20:44:36 views-feedback ERROR Traceback (most recent call last):

File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/django/core/handlers/base.py", line 83, in get_response
request.path_info)

File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/django/core/urlresolvers.py", line 233, in resolve
raise Resolver404, {'tried': tried, 'path': new_path}

Resolver404: {'path': u'', 'tried': ['^favicon\\.ico$', '^appmedia/webgateway/(?P<path>.*)$', '^appmedia/omeroweb/(?P<path>.*)$', '^appmedia/(?P<path>.*)$', '(?i)^webadmin/', '(?i)^webclient/', '(?i)^feedback/', '(?i)^webgateway/', '(?i)^webtest/']}

Thu, 02 Sep 2010 20:44:36 views-admin INFO INIT '19720'
Thu, 02 Sep 2010 20:44:36 views-web INFO INIT '19720'
Thu, 02 Sep 2010 20:44:45 views-admin INFO INIT '19723'
Thu, 02 Sep 2010 20:44:45 views-web INFO INIT '19723'

Thu, 02 Sep 2010 20:47:35 omero.util.UpgradeCheck INFO no update needed
Thu, 02 Sep 2010 20:47:35 webgateway INFO getBlitzConnection(host=localhost, port=4064, ssl=True, username=root)
Thu, 02 Sep 2010 20:47:35 webgateway ERROR Critical error during connect, retrying after _purge
Thu, 02 Sep 2010 20:47:35 webgateway INFO reached connector_pool_size (70), size after purge: (0)
Thu, 02 Sep 2010 20:47:35 webgateway ERROR Critical error during connect, retrying after _purge
Thu, 02 Sep 2010 20:47:35 webgateway INFO reached connector_pool_size (70), size after purge: (0)
Thu, 02 Sep 2010 20:47:35 views-admin INFO Have connection as Guest
Thu, 02 Sep 2010 20:47:35 views-admin ERROR Traceback (most recent call last):
File "/usr/local/OMERO/lib/python/omeroweb/webadmin/views.py", line 100, in _checkVersion
agent = conn.getServerVersion()
AttributeError: 'NoneType' object has no attribute 'getServerVersion'

***************** end of log snippet *******************



================================================================================
OMERO Diagnostics Beta-4.2.0-r7571-b29
================================================================================

Commands: java -version 1.6.0 (/usr/bin/java)
Commands: python -V 2.6.5 (/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 8.3.9 (/opt/local/lib/postgresql83/bin/psql)

Server: icegridnode running
Server: Blitz-0 inactive (disabled)
Server: DropBox inactive (disabled)
Server: FileServer active (pid = 10886, enabled)
Server: Indexer-0 inactive (disabled)
Server: MonitorServer inactive (disabled)
Server: OMERO.Glacier2 inactive (disabled)
Server: OMERO.IceStorm inactive (disabled)
Server: Processor-0 activating (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: /usr/local/OMERO/var/log exists

Log files: Blitz-0.log 124.0 KB errors=3 warnings=27
Log files: DropBox.log 3.0 KB errors=6 warnings=0
Log files: FileServer.log 0.0 KB
Log files: Indexer-0.log 135.0 KB errors=3 warnings=27
Log files: MonitorServer.log 2.0 KB errors=3 warnings=0
Log files: OMEROweb.log 16.0 KB errors=50 warnings=0
Log files: Processor-0.log 4.0 MB errors=1228 warnings=8596
Log files: Tables-0.log n/a
Log files: TestDropBox.log n/a
Log files: master.err 1.0 KB
Log files: master.out 0.0 KB
Log files: Total size 4.73 MB


Environment:OMERO_HOME=(unset)
Environment:OMERO_NODE=(unset)
Environment:OMERO_MASTER=(unset)
Environment:PATH=/opt/local/bin:/opt/local/sbin:/sw/bin:/sw/sbin:/usr/bin:/bin:/usr \
/sbin:/sbin:/usr/local/bin:/usr/X11/bin:/usr/ebiotools/bin: \
/usr/local/cisgenome_v1.2/bin:/opt/local/lib/postgresql83/bin:/usr/X11R6/bin
Environment:ICE_HOME=(unset)
Environment:LD_LIBRARY_PATH=(unset)
Environment:DYLD_LIBRARY_PATH=(unset)
*****************

Hi,

================================================================================
OMERO Diagnostics Beta-4.2.0-r7571-b29
================================================================================
...
Server: icegridnode running
Server: Blitz-0 inactive (disabled)
*****************

Blitz is the main server component. For some reasons, it's failed. Could you send us the var/log/Blitz-0.log?

Is this possibly due to the OMERO's insistence on using port 4064? And if so, how to I rectify the situation?

Also, I understand that even with SSL deselected in the login screen, the username and password are still encrypted. Is there something I need to configure in Apache to accommodate this? (I have no SSL certificate for this host).

I don't believe so. You don't need an SSL certificate since Ice uses anonymous SSL for the communication.

Let's figure out why your Blitz isn't working first, and then we can follow up on any other errors.
Cheers,
~Josh.

I've attached the Blitzz-0.log which includes the latest OMERO server shutdown and restart.

Following my post earlier this moring, I re-ran the OMERO diagnostics and it appears that blitz is running, but I'm still experiencing the same inability to log in to the webadmin root account as described in my original post. Here's my latest diagnostics output:

gnbch100:~ admin$ /usr/local/OMERO/bin/omero admin diagnostics

================================================================================
OMERO Diagnostics Beta-4.2.0-r7571-b29
================================================================================

Commands: java -version 1.6.0 (/usr/bin/java)
Commands: python -V 2.6.5 (/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 8.3.9 (/opt/local/lib/postgresql83/bin/psql)

Server: icegridnode running
Server: Blitz-0 active (pid = 78507, enabled)
Server: DropBox inactive (disabled)
Server: FileServer active (pid = 78509, enabled)
Server: Indexer-0 active (pid = 78510, enabled)
Server: MonitorServer inactive (disabled)
Server: OMERO.Glacier2 inactive (disabled)
Server: OMERO.IceStorm inactive (disabled)
Server: Processor-0 active (pid = 78514, 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: /usr/local/OMERO/var/log exists

Log files: Blitz-0.log 3.0 MB errors=3 warnings=3995
Log files: DropBox.log 8.0 KB errors=14 warnings=0
Log files: FileServer.log 2.0 KB
Log files: Indexer-0.log 212.0 KB errors=3 warnings=63
Log files: MonitorServer.log 5.0 KB errors=7 warnings=0
Log files: OMEROweb.log 28.0 KB errors=85 warnings=0
Log files: Processor-0.log 4.0 MB errors=1138 warnings=7969
Log files: Processor-0.log.1 4.0 MB errors=1381 warnings=9667
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 13.18 MB

Parsing Blitz-0.log:[line:527] => Server restarted <=
Parsing Blitz-0.log:[line:793] => Server restarted <=
Parsing Blitz-0.log:[line:1778] => Server restarted <=
Parsing Blitz-0.log:[line:40076] => Server restarted <=

Environment:OMERO_HOME=(unset)
Environment:OMERO_NODE=(unset)
Environment:OMERO_MASTER=(unset)
Environment:PATH=/opt/local/bin:/opt/local/sbin:/sw/bin:/sw/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin:/usr/ebiotools/bin:/usr/local/cisgenome_v1.2/bin:/opt/local/lib/postgresql83/bin:/usr/X11R6/bin
Environment:ICE_HOME=(unset)
Environment:LD_LIBRARY_PATH=(unset)
Environment:DYLD_LIBRARY_PATH=(unset)


and the latest OMEROweb.log entries:

Fri, 03 Sep 2010 18:47:39 webgateway ERROR Critical error during connect, retrying after _purge
Fri, 03 Sep 2010 18:47:39 webgateway INFO reached connector_pool_size (70), size after purge: (0)
Fri, 03 Sep 2010 18:47:39 views-admin INFO Have connection as Guest
Fri, 03 Sep 2010 18:47:39 views-admin ERROR Traceback (most recent call last):
File "/usr/local/OMERO/lib/python/omeroweb/webadmin/views.py", line 100, in _checkVersion
agent = conn.getServerVersion()
AttributeError: 'NoneType' object has no attribute 'getServerVersion'

Fri, 03 Sep 2010 18:47:39 views-web INFO INIT '36642'
Tue, 07 Sep 2010 18:24:55 views-admin INFO INIT '78863'
Tue, 07 Sep 2010 18:24:57 omero.util.UpgradeCheck INFO no update needed
Tue, 07 Sep 2010 18:24:57 webgateway INFO getBlitzConnection(host=localhost, port=4064, ssl=True, username=root)
Tue, 07 Sep 2010 18:24:57 webgateway ERROR Critical error during connect, retrying after _purge
Tue, 07 Sep 2010 18:24:57 webgateway INFO reached connector_pool_size (70), size after purge: (0)
Tue, 07 Sep 2010 18:24:57 webgateway ERROR Critical error during connect, retrying after _purge
Tue, 07 Sep 2010 18:24:57 webgateway INFO reached connector_pool_size (70), size after purge: (0)
Tue, 07 Sep 2010 18:24:57 views-admin INFO Have connection as Guest
Tue, 07 Sep 2010 18:24:57 views-admin ERROR Traceback (most recent call last):
File "/usr/local/OMERO/lib/python/omeroweb/webadmin/views.py", line 100, in _checkVersion
agent = conn.getServerVersion()
AttributeError: 'NoneType' object has no attribute 'getServerVersion'

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


As I indicated on one of my follow-up posts, my Blitz server is, in fact, running. The only suspicious thing(s) that I can see from the diagnostics output is that the OMERO.Glacier2 and OMERO.IceStorm servers are not running. I don't know whether these are at the heart of my connection failure nor how to get them running if that's what's needed.

Could you possibly post the contents of var/log/master.out and var/log/master.err? Without the router running there's no way to contact the server.

~Josh.

I've attached the master.err file and the master.out file was empty.

Code: Select all

09/01/10 16:35:11.825 OMERO.IceStorm: error: ServiceManager: unable to load entry point `IceStormService,33:createIceStorm': dlopen(libIceStormService.33.dylib, 10)>
09/01/10 16:35:11.852 OMERO.Glacier2: error: service caught unhandled exception:
PluginManagerI.cpp:352: Ice::PluginInitializationException:
plug-in initialization failed: unable to load entry point `IceSSL:createIceSSL': dlopen(libIceSSL.33.dylib, 10): image not found


Can you try calling:

Code: Select all

bin/omero admin stop
export DYLD_LIBRARY_PATH=/opt/local/lib
bin/omero admin start


Cheers,
~Josh

That got OMERO.Glacier2 and OMERO.IceStorm running, but the server start "Failed to start after 5 minutes" and the diagnostics now show taht Blitz-0 is not running and Procesor-0 activation timed out:


I've attached the Blitz-0.log and Processor-0.log entries from today.

================================================================================
OMERO Diagnostics Beta-4.2.0-r7571-b29
================================================================================

Commands: java -version 1.6.0 (/usr/bin/java)
Commands: python -V 2.6.5 (/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 8.3.9 (/opt/local/lib/postgresql83/bin/psql)

Server: icegridnode running
Server: Blitz-0 inactive (disabled)
Server: DropBox inactive (disabled)
Server: FileServer active (pid = 91713, enabled)
Server: Indexer-0 inactive (disabled)
Server: MonitorServer inactive (disabled)
Server: OMERO.Glacier2 active (pid = 91716, enabled)
Server: OMERO.IceStorm active (pid = 91717, enabled)
Server: Processor-0 activation timed out (pid = 91801, 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: /usr/local/OMERO/var/log exists

Log files: Blitz-0.log 4.0 MB errors=3 warnings=5116
Log files: DropBox.log 10.0 KB errors=20 warnings=0
Log files: FileServer.log 3.0 KB
Log files: Indexer-0.log 230.0 KB errors=3 warnings=63
Log files: MonitorServer.log 7.0 KB errors=10 warnings=0
Log files: OMEROweb.log 29.0 KB errors=88 warnings=0
Log files: Processor-0.log 4.0 MB errors=1159 warnings=8117
Log files: Processor-0.log.1 4.0 MB errors=1381 warnings=9667
Log files: Tables-0.log n/a
Log files: TestDropBox.log n/a
Log files: master.err 6.0 KB
Log files: master.out 0.0 KB
Log files: Total size 14.31 MB

Parsing Blitz-0.log:[line:527] => Server restarted <=
Parsing Blitz-0.log:[line:793] => Server restarted <=
Parsing Blitz-0.log:[line:1778] => Server restarted <=
Parsing Blitz-0.log:[line:40076] => Server restarted <=

Environment:OMERO_HOME=(unset)
Environment:OMERO_NODE=(unset)
Environment:OMERO_MASTER=(unset)
Environment:PATH=/opt/local/bin:/opt/local/sbin:/sw/bin:/sw/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin:/usr/ebiotools/bin:/usr/local/cisgenome_v1.2/bin:/opt/local/lib/postgresql83/bin:/usr/X11R6/bin
Environment:ICE_HOME=(unset)
Environment:LD_LIBRARY_PATH=(unset)
Environment:DYLD_LIBRARY_PATH=(unset)
gnbch100:~ admin$

Could there be some mixup with the logs? The diagnostics say that there are 3 error messages for Blitz-0.log, but I can't find them (and the file is only 600K and not 4 MB). Could you try:

Code: Select all

bin/omero admin stop # shutdown the server
rm -rf var                   # remove all the logs
export DYLD_LIBRARY_PATH=/opt/local/lib # Make sure this is still set
bin/omero admin start


If the server still fails to startup, then it will be clearer what's from this latest attempt and what is from earlier today.

Sorry for the hassle,
~Josh.

Sorry, I should have made it more clear that the log records in my last post were just those of the day, not the entire log file.

I've shut everything down, rebooted the machine, wiped the log directory as you instructed. I then set the DYLD_LIBRARY_PATH variable as instructed and again the Blitz-0 server failed to startup. Here's the subsquent diagnostic output and I've attached ALL of the logs.

Thanks again for working through this with me.

================================================================================
OMERO Diagnostics Beta-4.2.0-r7571-b29
================================================================================

Commands: java -version 1.6.0 (/usr/bin/java)
Commands: python -V 2.6.5 (/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 8.3.9 (/opt/local/lib/postgresql83/bin/psql)

Server: icegridnode running
Server: Blitz-0 inactive (disabled)
Server: DropBox inactive (disabled)
Server: FileServer active (pid = 475, enabled)
Server: Indexer-0 inactive (disabled)
Server: MonitorServer inactive (disabled)
Server: OMERO.Glacier2 active (pid = 478, enabled)
Server: OMERO.IceStorm active (pid = 479, enabled)
Server: Processor-0 activating (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: /usr/local/OMERO/var/log exists

Log files: Blitz-0.log n/a
Log files: DropBox.log 0.0 KB errors=2 warnings=0
Log files: FileServer.log 0.0 KB
Log files: Indexer-0.log n/a
Log files: MonitorServer.log 0.0 KB errors=1 warnings=0
Log files: OMEROweb.log n/a
Log files: Processor-0.log 18.0 KB errors=5 warnings=35
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 0.02 MB

Error while parsing logs

Environment:OMERO_HOME=(unset)
Environment:OMERO_NODE=(unset)
Environment:OMERO_MASTER=(unset)
Environment:PATH=/opt/local/bin:/opt/local/sbin:/sw/bin:/sw/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin:/usr/ebiotools/bin:/usr/local/cisgenome_v1.2/bin:/opt/local/lib/postgresql83/bin:/usr/X11R6/bin
Environment:ICE_HOME=(unset)
Environment:LD_LIBRARY_PATH=(unset)
Environment:DYLD_LIBRARY_PATH=(unset)