Open Microscopy Environment

Posted: **Fri Apr 16, 2010 6:03 pm**

I thought successfully installed the omero.server and omero webadmin.
And I saw those were working once.

I installed the omero.web after my cluster computer administrator setup the apache with mod_python by following http://www.openmicroscopy.org.uk/site/support/omero4/server/archives/4.0/install-web
but I cannot login to the webadmin from another computer (not the computer that the omero.server and omero.web are installed).

when I tried to start the Web, it becomes dead very soon. like the followings

$ bin/omero admin ice
Ice 3.3.0 Copyright 2003-2008 ZeroC, Inc.
>>> server enable Web
>>> server start Web
>>> server state Web
active (pid = 19375, enabled)
>>> server state Web
inactive (enabled)

when I see the diagnostics by bin/omero admin diagnostics,
I see 2 errors from DropBox and 2 errors fro Processor-0.
and those are something like

2010-04-16 13:23:47,984 ERROR [ omero.util.TempFileManager] (MainThread) rmtree error: remove('/afs/cs.cmu.edu/user/bhcho/omero/tmp/omero_bhcho/10775/.lock') => [Errno 13] Permission denied: '/afs/cs.cmu.edu/user/bhcho/omero/tmp/omero_bhcho/10775/.lock'
2010-04-16 13:23:47,984 ERROR [ omero.util.TempFileManager] (MainThread) rmtree error: rmdir('/afs/cs.cmu.edu/user/bhcho/omero/tmp/omero_bhcho/10775') => [Errno 13] Permission denied: '/afs/cs.cmu.edu/user/bhcho/omero/tmp/omero_bhcho/10775'

/afs/cs.cmu.edu/user/bhcho/
is the home directory of my account on the machine.

Maybe this happens because I could not confugure "mod_pytnon" from the installation instruction (at the bottom of http://www.openmicroscopy.org.uk/site/support/omero4/server/archives/4.0/install-web)
Because I did not setup the apache with mod_python, I don't know where to configure.

Can anyone help me out here?

Posted: **Mon Apr 19, 2010 10:30 am**

Is this still on the same Linux machine? If you've deployed OMERO.web using mod_python you must disable the standalone OMERO.web service as described in on the Web on production page.

You also may have inadvertently produced log files that have the wrong permissions. What's currently in your settings.py for OMERO.web?

Posted: **Mon Apr 19, 2010 2:29 pm**

thanks cxallan,

yes it's still on the same Linux machine.
do you mean the disablement like below?

$ cd /home/omero/omero_dist/
$ bin/omero admin ice
Ice 3.3.0 Copyright 2003-2008 ZeroC, Inc.
>>> server disable Web
>>> server stop Web

if so, yes I did.

and here I attached all log files and the setting.py file

logs.tar.bz2: (7.66 KiB) Downloaded 269 times

Posted: **Mon Apr 19, 2010 4:13 pm**

bhcho wrote:thanks cxallan,

yes it's still on the same Linux machine.
do you mean the disablement like below?

$ cd /home/omero/omero_dist/
$ bin/omero admin ice
Ice 3.3.0 Copyright 2003-2008 ZeroC, Inc.
>>> server disable Web
>>> server stop Web

if so, yes I did.

No. You need to ensure that it never starts via etc/grid/default.xml:

Code: Select all: ... <server-instance template="ShellTemplate" id="Web" act="on-demand"/> ...

If you've done this then I need to see the output of:

Code: Select all: ls -al '/usr0/local/omero.server/weblog/' ls -al '/usr0/local/omero.server/webdb/db.sqlite3'

Once you've set up OMERO.web to work through mod_python you must not attempt to start it via bin/omero admin ice or you risk creating log files and SQLite database files that have incorrect permissions.

Posted: **Mon Apr 19, 2010 4:47 pm**

I set the etc/grid/default.xml as

<server-instance template="ShellTemplate" id="Web" act="on-demand"/>

and the outputs are

$ ls -al '/usr0/local/omero.server/weblog/'
total 16
drwxrwxrwx 2 bhcho users 4096 2010-04-16 13:32 .
drwxrwxrwx 5 root root 4096 2010-04-16 10:08 ..
-rw-r--r-- 1 root root 75 2010-04-16 13:32 OMEROweb.log
-rw-r--r-- 1 root root 221 2010-04-16 13:32 OMEROweb.log.2010-04-16

$ ls -al '/usr0/local/omero.server/webdb/db.sqlite3'
-rw-r--r-- 1 root root 33792 2010-04-16 13:32 /usr0/local/omero.server/webdb/db.sqlite3

could you tell me what should I do now?

Posted: **Mon Apr 19, 2010 4:51 pm**

All those files and directories must be owned by the user who is running Apache.

Posted: **Mon Apr 19, 2010 5:17 pm**

Thank you so much again,

after I changed the ownership to the user that runs the Apache, and run the server again with ice command (server enable/start Web),
Now I can login to the Webadmin and Webclient.

But when I see the /var/log/master.err,
the file size keeps increasing like below.

it seems like the Address already in use. Could you tell me what's wrong with this?

04/19/10 10:16:22.262 OMERO.Glacier2: error: service caught unhandled exception:
Network.cpp:1081: Ice::SocketException:
socket exception: Address already in use
Traceback (most recent call last):
File "lib/python/runTables.py", line 13, in <module>
__import__("tables")
File "/usr/lib64/python2.5/site-packages/tables/__init__.py", line 56, in <module>
from tables.utilsExtension import getPyTablesVersion, getHDF5Version
ImportError: libhdf5.so.6: cannot open shared object file: No such file or directory
04/19/10 10:16:22.771 OMERO.Glacier2: error: service caught unhandled exception:
Network.cpp:1081: Ice::SocketException:
socket exception: Address already in use
04/19/10 10:16:23.281 OMERO.Glacier2: error: service caught unhandled exception:
Network.cpp:1081: Ice::SocketException:
socket exception: Address already in use
Apr 19, 2010 10:16:23 AM java.util.prefs.FileSystemPreferences$7 run
WARNING: Prefs file removed in background /afs/cs.cmu.edu/misc/java/amd64_f10/jdk1.6.0_16/libexec/jdk1.6.0_16-64bit/jre/.systemPrefs/prefs.xml
Apr 19, 2010 10:16:23 AM java.util.prefs.FileSystemPreferences$7 run
WARNING: Prefs file removed in background /afs/cs.cmu.edu/misc/java/amd64_f10/jdk1.6.0_16/libexec/jdk1.6.0_16-64bit/jre/.systemPrefs/prefs.xml
04/19/10 10:16:23.790 OMERO.Glacier2: error: service caught unhandled exception:
Network.cpp:1081: Ice::SocketException:
socket exception: Address already in use
04/19/10 10:16:24.298 OMERO.Glacier2: error: service caught unhandled exception:
Network.cpp:1081: Ice::SocketException:
socket exception: Address already in use
04/19/10 10:16:24.812 OMERO.Glacier2: error: service caught unhandled exception:
Network.cpp:1081: Ice::SocketException:
socket exception: Address already in use
04/19/10 10:16:25.323 OMERO.Glacier2: error: service caught unhandled exception:
Network.cpp:1081: Ice::SocketException:
socket exception: Address already in use
....samething kepp going

Posted: **Mon Apr 19, 2010 5:23 pm**

As I said above, once you are running under mod_python with Apache DO NOT run bin/omero admin ice (enable/start Web). You WILL corrupt permissions this way. OMERO.web when running under mod_python with Apache is started when Apache starts.

Posted: **Wed Apr 21, 2010 1:57 pm**

I see. now I understand I should have not followed the OMERO.web instruction from
http://www.openmicroscopy.org.uk/site/support/omero4/server/installation
Insead, I had to follow the http://www.openmicroscopy.org.uk/site/support/omero4/server/install_web since I installed the apache with mod_python.

okay then, as I said, since I did not install the Apache with mod_python on my server by myself (my administrator did), could you tell me any idea how to start the Apache and more importantly how to (or where to) configure the mod_python like below?

<Location "/">
SetHandler python-program
PythonHandler django.core.handlers.modpython
SetEnv DJANGO_SETTINGS_MODULE omeroweb.settings
PythonDebug On
PythonPath "['/home/omero/omero_dist/lib/python', '/home/omero/omero_dist/lib/python/omeroweb] + sys.path"

</Location>

Posted: **Wed Apr 21, 2010 5:45 pm**

I somehow started the Apache2 on my server and configured the mod_python by editting httpd.conf file adding the following lines at the end of the file.

<Location "/">
SetHandler python-program
PythonHandler django.core.handlers.modpython
SetEnv DJANGO_SETTINGS_MODULE omeroweb.settings
PythonDebug On
PythonPath "['/home/omero/omero_dist/lib/python', '/home/omero/omero_dist/lib/python/omeroweb] + sys.path"

</Location>

and I restarted my OMERO.server by bin/omero admin start
But, still I cannot logon to omero web http://your_host/webclient/ nor http://your_host/webadmin/.
when I look at the master.err file, I have the foolowing errors

04/21/10 13:38:56.382 OMERO.Glacier2: error: service caught unhandled exception:
Network.cpp:1081: Ice::SocketException:
socket exception: Address already in use
Traceback (most recent call last):
File "lib/python/runTables.py", line 13, in <module>
__import__("tables")
File "/usr/lib64/python2.5/site-packages/tables/__init__.py", line 56, in <module>
from tables.utilsExtension import getPyTablesVersion, getHDF5Version
ImportError: libhdf5.so.6: cannot open shared object file: No such file or directory
04/21/10 13:38:56.891 OMERO.Glacier2: error: service caught unhandled exception:
Network.cpp:1081: Ice::SocketException:
socket exception: Address already in use
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
04/21/10 13:38:57.913 OMERO.Glacier2: error: service caught unhandled exception:
Network.cpp:1081: Ice::SocketException:
socket exception: Address already in use
Apr 21, 2010 1:38:57 PM java.util.prefs.FileSystemPreferences$7 run
WARNING: Prefs file removed in background /afs/cs.cmu.edu/misc/java/amd64_f10/jdk1.6.0_16/libexec/jdk1.6.0_16-64bit/jre/.systemPrefs/prefs.xml
Apr 21, 2010 1:38:57 PM java.util.prefs.FileSystemPreferences$7 run
WARNING: Prefs file removed in background /afs/cs.cmu.edu/misc/java/amd64_f10/jdk1.6.0_16/libexec/jdk1.6.0_16-64bit/jre/.systemPrefs/prefs.xml
04/21/10 13:38:58.424 OMERO.Glacier2: error: service caught unhandled exception:
Network.cpp:1081: Ice::SocketException:
socket exception: Address already in use
04/21/10 13:38:58.935 OMERO.Glacier2: error: service caught unhandled exception:
Network.cpp:1081: Ice::SocketException:
socket exception: Address already in use
04/21/10 13:38:59.445 OMERO.Glacier2: error: service caught unhandled exception:
Network.cpp:1081: Ice::SocketException:
socket exception: Address already in use
.... the same messages keep going

Could you tell me any idea on this?

Open Microscopy Environment

omero.server and omero.web

omero.server and omero.web

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Re: omero.server and omero.web

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Re: omero.server and omero.web

Re: omero.server and omero.web

Re: omero.server and omero.web

Re: omero.server and omero.web

Re: omero.server and omero.web

Re: omero.server and omero.web