Open Microscopy Environment

Everything seems to have gone smoothly with the server setup on Ubuntu 10.0 , no error messages, and the server seems to initialize fine, but then when I try to login from another machine on the network it will not let me in. Do I have to run the web server? We would prefer to keep our files with local only access.

One detail that did come up when I examine the pqsl database:

$ psql -h localhost -U omero -1
Password for user omero:
psql (8.4.4)
SSL connection (cipher: DHE-RSA-AES256-SHA, bits: 256)
Type "help" for help.


Instead of what was shown on the webpage. Is this due to using version 8.4.4?

Thanks again

No, you don't have to have any web server started unless you want to use OMERO.web. Have you checked the firewall on your Ubuntu machine? Are there other firewalls on your network? How are you connecting? Which client are you using?

As far as the firewall goes, on Ubuntu it is by default disabled, and I have not added any other. We are able to freely transfer files across our network here, although there are some security protocols that I may need to speak with the IT department about. I am trying to connect to the 4.2.0 server using the 4.2.0 client, and using the IP address of the system I am trying to access. The exact error message I receive is: Failed to log onto OMERO. Please check your username and/or password or try again later. I get this message whether the server is running or not. I will try to run both systems off of the same router, to see if there is some strange connection issue. Any other suggestions?

Have a look at your omeroinsight.log to see a more detailed error message. Feel free to attach it here. It should be in $HOME/omero/log.

Here is the omeroinsight.log file from my mac. Should I try to run insight on the same computer to see if I can bypass network restrictions?

That log file unfortunately does not show any attempted logins. You've set the host correctly by clicking on the wrench, etc. and entered in the username and password?

I can't even access the demo server, so at this point I think the problem is my University firewall. I am in communications with our network people to see if I can have access to the ports that we need. Otherwise, I imagine all I need to do is change the port settings. Could you tell me how to do this with the server software running in Ubuntu?

Thanks for all the help...

Sure. You can use a utility script from your OMERO.server install directory to do it:

Code: Select all

...
$ PYTHONPATH=lib/python python lib/python/omero/install/change_ports.py
$ lib/python/omero/install/change_ports.py [--revert] <glacier2 port> <icegrid registry port> [<glacier2 insecure port>]

    Changes all 4064 ports to the given glacier2 port
    and all 4061 ports to the given registry port. You will
    need to give your clients the new glacier2 port
...


There are many moving parts to port changes, so you should do so with caution.

According to our in house network people we should be able to access any port behind the firewall, so that shouldn't be the problem. I have run diagnostics, and here are the results.

Code: Select all

================================================================================
OMERO Diagnostics Beta-4.2.0-r7571-b29
================================================================================
       
Commands:   java -version                  1.6.0     (/usr/bin/java)
Commands:   python -V                      2.6.5     (/usr/bin/python)
Commands:   icegridnode --version          3.3.1     (/usr/bin/icegridnode)
Commands:   icegridadmin --version         3.3.1     (/usr/bin/icegridadmin)
Commands:   psql --version                 8.4.4     (/usr/bin/psql)

Server:     icegridnode                    running
Server:     Blitz-0                        active (pid = 2835, enabled)
Server:     DropBox                        active (pid = 2844, enabled)
Server:     FileServer                     active (pid = 2848, enabled)
Server:     Indexer-0                      active (pid = 2846, enabled)
Server:     MonitorServer                  active (pid = 2853, enabled)
Server:     OMERO.Glacier2                 active (pid = 2856, enabled)
Server:     OMERO.IceStorm                 active (pid = 2855, enabled)
Server:     Processor-0                    active (pid = 2850, 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:    /home/labpeople/omero_dist/var/log exists

Log files:  Blitz-0.log                    96.0 KB       errors=7    warnings=32 
Log files:  DropBox.log                    6.0 KB        errors=4    warnings=2   
Log files:  FileServer.log                 0.0 KB       
Log files:  Indexer-0.log                  155.0 KB      errors=5    warnings=28 
Log files:  MonitorServer.log              4.0 KB        errors=6    warnings=2   
Log files:  OMEROweb.log                   n/a
Log files:  Processor-0.log                38.0 KB       errors=10   warnings=70 
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                     0.30 MB

Parsing Blitz-0.log:[line:69] => Server restarted <=
Parsing Blitz-0.log:[line:490] Your database configuration is invalid
Parsing Blitz-0.log:[line:498] Your database configuration is invalid
Parsing Blitz-0.log:[line:517] Your database configuration is invalid
Parsing Blitz-0.log:[line:532] Your database configuration is invalid
Parsing Blitz-0.log:[line:540] Your database configuration is invalid
Parsing Blitz-0.log:[line:563] Your database configuration is invalid
Parsing Blitz-0.log:[line:681] => Server restarted <=

Environment:OMERO_HOME=(unset)             
Environment:OMERO_NODE=(unset)             
Environment:OMERO_MASTER=(unset)           
Environment:PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
Environment:ICE_HOME=(unset)               
Environment:LD_LIBRARY_PATH=(unset)       
Environment:DYLD_LIBRARY_PATH=(unset)

Okay, then back to the drawing board. Start up OMERO.insight on your client machine and make a connection attempt. Then attach $HOME/omero/log/omeroinsight.log from the client and /home/labpeople/omero_dist/var/log from the server.