Open Microscopy Environment

Posted: **Thu Apr 22, 2010 12:18 pm**

I'm now quite confused. Did you ever have Apache with mod_python working?

You can ignore what is in master.err it has nothing to do with your OMERO.web problems. You'll need to look in your configured OMERO.web configured log file directory and/or Apache logs to see what would be causing it to not start up or login.

Do you see anything when you navigate to http://your_host/webclient/ in your web browser?

Posted: **Thu Apr 22, 2010 2:12 pm**

This is the results when I navigate http://my_host/webclient/ in the web browser.

MOD_PYTHON ERROR

ProcessId: 28919
Interpreter: 'OMEPSLID.COMPBIO.CS.CMU.EDU'

ServerName: 'OMEPSLID.COMPBIO.CS.CMU.EDU'
DocumentRoot: '/usr/apache2/htdocs'

URI: '/webclient'
Location: '/'
Directory: None
Filename: '/usr/apache2/htdocs/webclient'
PathInfo: ''

Phase: 'PythonHandler'
Handler: 'django.core.handlers.modpython'

Traceback (most recent call last):

File "/afs/cs.cmu.edu/local/python/amd64_f10/2.6.1/usr/cs/lib/python2.6/site-packages/mod_python/importer.py", line 1537, in HandlerDispatch

File "/afs/cs.cmu.edu/local/python/amd64_f10/2.6.1/usr/cs/lib/python2.6/site-packages/mod_python/importer.py", line 1229, in _process_target

File "/afs/cs.cmu.edu/local/python/amd64_f10/2.6.1/usr/cs/lib/python2.6/site-packages/mod_python/importer.py", line 1128, in _execute_target

File "/usr0/local/omero.server/omero_dist/lib/python/django/core/handlers/modpython.py", line 222, in handler
return ModPythonHandler()(req)

File "/usr0/local/omero.server/omero_dist/lib/python/django/core/handlers/modpython.py", line 195, in __call__
response = self.get_response(request)

File "/usr0/local/omero.server/omero_dist/lib/python/django/core/handlers/base.py", line 67, in get_response
response = middleware_method(request)

File "/usr0/local/omero.server/omero_dist/lib/python/django/middleware/common.py", line 72, in process_request
urlresolvers.resolve("%s/" % request.path_info)

File "/usr0/local/omero.server/omero_dist/lib/python/django/core/urlresolvers.py", line 244, in resolve
return get_resolver(urlconf).resolve(path)

File "/usr0/local/omero.server/omero_dist/lib/python/django/core/urlresolvers.py", line 180, in resolve
sub_match = pattern.resolve(new_path)

File "/usr0/local/omero.server/omero_dist/lib/python/django/core/urlresolvers.py", line 178, in resolve
for pattern in self.urlconf_module.urlpatterns:

File "/usr0/local/omero.server/omero_dist/lib/python/django/core/urlresolvers.py", line 197, in _get_urlconf_module
self._urlconf_module = __import__(self.urlconf_name, {}, {}, [''])

File "/usr0/local/omero.server/omero_dist/lib/python/omeroweb/webclient/urls.py", line 30, in <module>
from omeroweb.webclient import views

File "/usr0/local/omero.server/omero_dist/lib/python/omeroweb/webclient/views.py", line 36, in <module>
import Ice

ImportError: No module named Ice

Posted: **Thu Apr 22, 2010 3:20 pm**

You need to add Ice, wherever you have installed it, to the mod_python PythonPath entry in your httpd.conf.

Posted: **Fri Apr 23, 2010 11:32 pm**

hi,

there is an error in your configuration:

Code: Select all: <Location "/"> ... PythonPath "['/home/omero/omero_dist/lib/python', '/home/omero/omero_dist/lib/python/omeroweb] + sys.path" ... </Location>

it must look like this:

Code: Select all: PythonPath "['/home/omero/omero_dist/lib/python', '/home/omero/omero_dist/lib/python/omeroweb'] + sys.path"

you have forgot the ' at the end of the second part in [ , ].

bye
michael

Posted: **Fri Apr 30, 2010 7:36 pm**

Thanks all,

I just decided not to use the OMERO.web production mode (using Apache2 with mod_python).

And the Ice Socket errors that says

04/21/10 13:38:57.402 OMERO.Glacier2: error: service caught unhandled exception:
Network.cpp:1081: Ice::SocketException:
socket exception: Address already in use

are solved by updating the Ice into version 3.3.1 from 3.3.0.

But still after a while, my server goes down.
When running, the diagostics are

================================================================================
OMERO Diagnostics Beta-4.1.1-r5927-b91
================================================================================

Commands: java -version 1.6.0 (/usr/local/bin/java -- 2 others)
Commands: python -V 2.5.2 (/usr/bin/python)
Commands: icegridnode --version 3.3.1 (/usr/bin/icegridnode)
Commands: icegridadmin --version 3.3.1 (/usr/bin/icegridadmin)
Commands: psql --version 8.3.4 (/usr/bin/psql)

Server: icegridnode running
Server: Blitz-0 active (pid = 9341, enabled)
Server: DropBox active (pid = 9360, enabled)
Server: FSServer active (pid = 9364, enabled)
Server: Indexer-0 active (pid = 9362, enabled)
Server: OMERO.Glacier2 active (pid = 9378, enabled)
Server: OMERO.IceStorm active (pid = 9380, enabled)
Server: Processor-0 active (pid = 9389, enabled)
Server: Tables-0 active (pid = 9391, enabled)
Server: TestDropBox inactive (enabled)
Server: Web active (pid = 9395, enabled)

Log dir: /usr0/local/omero.server/omero_dist/var/log exists

Log files: Blitz-0.log 216.0 KB errors=0 warnings=4
Log files: DropBox.log 1.0 KB
Log files: FSServer.log 1.0 KB
Log files: Indexer-0.log 4.0 KB errors=0 warnings=1
Log files: OMEROweb.log 0.0 KB
Log files: OMEROweb.log.2010-04-30 0.0 KB
Log files: Processor-0.log 0.0 KB
Log files: Tables-0.log 0.0 KB
Log files: TestDropBox.log n/a
Log files: master.err 2.0 KB errors=0 warnings=2
Log files: master.out 0.0 KB
Log files: Total size 0.23 MB

after I stop and the diagnostics are

================================================================================
OMERO Diagnostics Beta-4.1.1-r5927-b91
================================================================================

Commands: java -version 1.6.0 (/usr/local/bin/java -- 2 others)
Commands: python -V 2.5.2 (/usr/bin/python)
Commands: icegridnode --version 3.3.1 (/usr/bin/icegridnode)
Commands: icegridadmin --version 3.3.1 (/usr/bin/icegridadmin)
Commands: psql --version 8.3.4 (/usr/bin/psql)

Server: icegridnode running
Server: Blitz-0 deactivating (enabled)
Server: DropBox inactive (disabled)
Server: FSServer inactive (disabled)
Server: Indexer-0 inactive (disabled)
Server: OMERO.Glacier2 inactive (disabled)
Server: OMERO.IceStorm inactive (disabled)
Server: Processor-0 inactive (disabled)
Server: Tables-0 inactive (disabled)
Server: TestDropBox inactive (enabled)
Server: Web inactive (disabled)

Log dir: /usr0/local/omero.server/omero_dist/var/log exists

Log files: Blitz-0.log 222.0 KB errors=0 warnings=5
Log files: DropBox.log 3.0 KB errors=2 warnings=1
Log files: FSServer.log 1.0 KB
Log files: Indexer-0.log 4.0 KB errors=0 warnings=1
Log files: OMEROweb.log 0.0 KB
Log files: OMEROweb.log.2010-04-30 0.0 KB
Log files: Processor-0.log 2.0 KB errors=2 warnings=1
Log files: Tables-0.log 1.0 KB errors=0 warnings=1
Log files: TestDropBox.log n/a
Log files: master.err 3.0 KB errors=0 warnings=2
Log files: master.out 0.0 KB
Log files: Total size 0.24 MB

I attached the log files.
Does anyone have any idea? I dont think any firewalling service is running on my machine
Do I still need to do the /etc/hosts stuff and iptables stuff?

BK

Posted: **Mon May 03, 2010 2:48 pm**

I've seen the error before, but I'm not sure how to solve it. It seems to be a problem with the threading of the program though.

Posted: **Wed May 19, 2010 12:55 pm**

bhcho wrote:
...

But still after a while, my server goes down.

...

I attached the log files.
Does anyone have any idea? I dont think any firewalling service is running on my machine
Do I still need to do the /etc/hosts stuff and iptables stuff?

BK

What goes down?

No, you don't need any of the /etc/hosts modifications. You'll only need to perform the iptables changes if you have a firewall set up.

Posted: **Mon May 24, 2010 2:14 pm**

Thanks.

As I said,
after a while, I cannot connect to the server through the OMERO.insight,
like the error in the troubleshooting link. ( The "Remote clients can't connect to my OMERO installation!" part)
http://www.openmicroscopy.org/site/support/omero4/server/troubleshooting

But I still can connect to the server through the OMERO.importer.
It looks weird. I don't have any firewall configuration.

BK

Posted: **Mon May 24, 2010 2:46 pm**

From a more in depth look at the log files it appears that you end up with some rather nasty locking issues with files in your OMERO root and JVM directories. Are these on shared storage? Where are /usr0/, /home, etc.?

Posted: **Mon May 24, 2010 6:16 pm**

you end up with some rather nasty locking issues with files in your OMERO root and JVM directories. Are these on shared storage? Where are /usr0/, /home, etc.?

I'm not sure how to answer this question, but

1.
if you are refering to OMERO root as the 'omero_dist' directory, then it's
/usr0/local/omero.server/omero_dist
and the directory permission is drwxr-xr-x (do I need to change it ?)

And the OMERO binary repository location is
/usr1/OMERO whose permission is drwxrwxrwx.

2.
I see a /etc/jvm and a /usr/share/jvm. There are other directories as well. I'm not sure which one is the "right" one.
3.
for the home directory, it's little bit uncommon.
when I log into the server, the current directory seems on a shared storage (not sure and will ask this to my administrator). And those directory of "omero/tmp/omero_bhcho/" are within this home directory.
But those /usr0 and /usr1 (where the omero_dist and repository reside) are on local storages.

4. when I command "$ cd /home"
then the 'pwd' commands shows me I'm in "/usr0" like below

Code: Select all: [@omepslid omero_dist]$ cd /home/ [@omepslid /home]$ pwd /usr0

Open Microscopy Environment

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Re: omero.server and omero.web