cannot log in to webadmin

[jmoore]

In master.out there's this:

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Error occurred during initialization of VM
Error occurred during initialization of VM
Unable to load native libraryUnable to load native library: libjava.jnilib
: libjava.jnilib
(END)


which points to a library conflict between MacPorts and your Apple's Java installation. The problem is described at http://stackoverflow.com/questions/1482450/broken-java-mac-10-6. Another user (Ronald Taylor) had a similar problem back in June: http://lists.openmicroscopy.org.uk/pipermail/ome-users/2010-June/002312.html.

There are several ways you could solve this. The first is to put the shadowed libraries first on your DYLD_LIBRARY_PATH. For example,

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


The second is to copy the necessary Ice libraries from /opt/local/lib to a second location and to set that value as your DYLD_LIBRARY_PATH. One final possibility is to not use the Ice libraries from MacPorts, but to compile Ice yourself. I've posted information for doing that on the ZeroC forums: http://www.zeroc.com/forums/help-center/5069-make-error.html#post22222

Cheers,
~Josh

[dpbrown]

Well, I apparently resolved the library conflict using your suggestion of copying the ice libraries to a new directory and setting the path to that directory. I now get Blitz, IceStorm, Glacier2, Fileserver, etc as well as Processor all to run and I can connect via web browser and bring up he Webadmin inerface, but still get the same "Error: Client version does not match server, please contact administrator." upon login as root.

I've attached another archive of all logs.


================================================================================
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 = 12172, enabled)
Server: DropBox inactive (disabled)
Server: FileServer active (pid = 12174, enabled)
Server: Indexer-0 active (pid = 12175, enabled)
Server: MonitorServer inactive (disabled)
Server: OMERO.Glacier2 active (pid = 12177, enabled)
Server: OMERO.IceStorm active (pid = 12178, enabled)
Server: Processor-0 active (pid = 12179, 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 144.0 KB errors=4 warnings=82
Log files: DropBox.log 8.0 KB errors=13 warnings=0
Log files: FileServer.log 2.0 KB
Log files: Indexer-0.log 17.0 KB errors=0 warnings=45
Log files: MonitorServer.log 5.0 KB errors=7 warnings=0
Log files: OMEROweb.log 2.0 KB errors=5 warnings=0
Log files: Processor-0.log 285.0 KB errors=77 warnings=539
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 0.47 MB

Parsing Blitz-0.log:[line:17] => Server restarted <=
Parsing Blitz-0.log:[line:197] => Server restarted <=
Parsing Blitz-0.log:[line:369] => Server restarted <=
Parsing Blitz-0.log:[line:631] => Server restarted <=
Parsing Blitz-0.log:[line:885] => Server restarted <=
Parsing Blitz-0.log:[line:1038] => 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)

[jmoore]

Well, you're certainly getting a new issue:

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09/09/10 17:15:52.111 icegridnode: error: failed to rollback previous application `OMERO':
couldn't load `FileServer' on node `master':
can't change permissions on `.':
Operation not permitted
09/09/10 17:15:52.112 icegridnode: warning: failed to deploy application `/usr/local/OMERO/etc/grid/default.xml':
IceGrid::DeploymentException: couldn't load `DropBox' on node `master':
can't change permissions on `.':


Did something happen to the permissions of your installation directory? Did it get deleted? (If so, is there an old instance of icegridnode running?) What does "ps auxww | grep icegridnode" show?
~Josh.

[dpbrown]

OK, In order to eliminate any legacy of permissions or compiled python code, I started all over with a new OMERO tarball which I extracted and followed through with a new installation.

Now, with the exception of the DropBox, MonitorServer and Repository-1 servers, everything appears to start up nicely and the logs look pretty error free. (see diagnostics.txt in attached archive)

I also created a new OMERO database initialization script, again with no problems. However, when I attempt to initialize my database with the script I get a long series of error messages (see db_initialize_errors.txt in attatched archive.

So, I'm thinking that maybe the problem I'm having logging in with the root password is that the initialization of the db with the OMERO root user pw isn't happening.

My database seems to be in place as I get the expected output from: ...$ psql -h localhost -U omero -l

List of databases
Name | Owner | Encoding
-----------+----------+----------
omero | omero | UTF8
postgres | postgres | UTF8
template0 | postgres | UTF8
template1 | postgres | UTF8
(4 rows)

Again, thanks for slogging through this with me.

[jmoore]

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gnbch100:OMERO admin$ psql -h localhost -U omero omero < OMERO4.2__0.sql
BEGIN
ERROR:  relation "acquisitionmode" already exists
ERROR:  current transaction is aborted, commands ign


This says that you didn't drop the "omero" database and recreate it, i.e. it already exists. That's not the worst thing in the world, but certainly not what you meant to happen.

Regardless, Blitz started cleanly. The issue may, then, actually be password related. You might take a look at the following sections:

• https://www.openmicroscopy.org/site/support/omero4/troubleshooting#section-3 - on which passwords to use where
• https://www.openmicroscopy.org/site/support/omero4/server/security - on how to reset the root password

Hope that helps.
~Josh.

[dpbrown]

I started all over yet again with a new OMERO tarball which I extracted and followed through with a new installation (even including a new OMERO binary repository). This time I created a new database with a unique name and user (omero3) and when I initialized this new db with the omero dp script all seemed to work just fine (terminal output included in attached archive).

Again, with the exception of the DropBox, MonitorServer and Repository-1 servers, everything appears to start up nicely and the logs look pretty error free. (see files in attached archive).

Still the same problem: I can connect to my host from a remote machine and I get the same message when I attempt to log in with the root user password I created when generating the omero db script.

My postgreSQL installation looks ok: listening on correct port, and the hba config should allow access, but I'm just not connecting.

Any suggestions would be much appreciated.

[atarkowska]

It looks like OMERO.web does not allow you to let in because is trying to create new connections over again. Could you please try to apply the attached patch by the following command:

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patch -p0 -i ~/OMERO.web_fix_bug_ticket_2853.diff

then restart Apache.
If you still cannot log in, please go to omero/var/lib/custom_settings.py and just before SERVER_LIST please add:

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DEBUG = True

restart Apache, and try to log in. Then send me the new log omero/var/log/OMEROweb-DEBUG.log

OMERO.web_fix_bug_ticket_2853.zip

(913 Bytes) Downloaded 226 times

[dpbrown]

Long delay in following up on the latest recommendation due to travel and the fact that I decided to start from scratch and have installed OMERO 4.2.0 on a brand new Snow Leopard Server, installing everything from source following the most excellent guide provided by Janek Claus and Kenneth Arcieri.

I've again succeeded in getting OMERO apparently up and running.

With the exception of DropBox, Repository-1 and TestDropBox, all the server components are running.

With a web browser, I can get to the Webadmin login , but when I attempt to log on as root I still get the "client version does not match server" error message.

I've attempted to apply the patch provided in the previous post, but am obviously doing something wrong. Using the command provided, I'm prompted to locate/identify the file to patch (views.py) and am not sure how to correctly specify the target file to patch. There are numerous "views.py" files within the omeroweb directory.

Here's the terminal output from my patch attempt:

host:user$ patch -p0 -i OMERO.web_fix_bug_ticket_2853.diff
can't find file to patch at input line 5
Perhaps you used the wrong -p or --strip option?
The text leading up to this was:
--------------------------
|Index: views.py
|===================================================================
|--- views.py (revision 7799)
|+++ views.py (working copy)
--------------------------
File to patch:

and when I specify the path to the copy of views.py in the webadmin directory, I get:

Hunk #1 FAILED at 214.
1 out of 1 hunk FAILED -- saving rejects to file .../OMERO/lib/python/omeroweb/webadmin/views.py.rej

Any suggestions would be apprectiated.