Open Microscopy Environment

Hi,

I have a question to set up 'LD_LIBRARY_PATH' .
someone installed ice and all application through rpm package.
so, I think that icestorm and glacier2 (3.3.1) are installed successfully through rpm package.
when I look at the diagnostic, both of them seems to work fine like you see below code.

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Server:     icegridnode                    running
Server:     Blitz-0                        active (pid = 19322, enabled)
Server:     DropBox                        inactive (disabled)
Server:     FileServer                     active (pid = 19349, enabled)
Server:     Indexer-0                      active (pid = 19352, enabled)
Server:     MonitorServer                  inactive (disabled)
Server:     OMERO.Glacier2                 active (pid = 19354, enabled)
Server:     OMERO.IceStorm                 active (pid = 19355, enabled)
Server:     Processor-0                    active (pid = 19357, enabled)
Server:     Repository-1                   error: node `repo' couldn't be reached:
the node is not active


Do I still should set up 'LD_LIBRARY_PATH' manually in the .bashrc profile ?
I have no idea where this library is located in the server.
How I can find the location of lib file to set up LD_LIBRARY ?
(someone else installed it through rpm (package))

Thanks,
Steve

Steve,

what condition are you seeing that you are trying to modify LD_LIBRARY_PATH to fix? RPM installs of the packages shouldn't require you to change any environment settings.

Cheers,
~Josh.

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[code]
# .bash_profile

# Get the aliases and functions
if [ -f ~/.bashrc ]; then
        . ~/.bashrc
fi

# User specific environment and startup programs

#PATH=$PATH:$HOME/bin
#export PATH

export PATH=/develop/software/java/jdk1.6.0_21/bin/:$PATH:/opt/ibm/db2/V9.7/bin:/usr/lib64/python2.3/site-packages/Ice/
export PYTHONPATH=$PYTHONPATH:/usr/lib64/python2.3/site-packages/Ice/
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib64/python2.3/site-packages/Ice/
[/code]

diagnostic result is like as follows.

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================================================================================
OMERO Diagnostics Beta4.2.2-r8718-Beta4.2-b56
================================================================================
       
Commands:   java -version                  1.6.0     (/develop/software/java/jdk1.6.0_21/bin/java -- 2 others)
Commands:   python -V                      2.4.3     (/usr/bin/python)
Commands:   icegridnode --version          3.3.1     (/usr/bin/icegridnode)
Commands:   icegridadmin --version         3.3.1     (/usr/bin/icegridadmin)
Commands:   psql --version                 8.1.22    (/usr/bin/psql)

Server:     icegridnode                    running
Server:     Blitz-0                        active (pid = 23186, enabled)
Server:     DropBox                        inactive (disabled)
Server:     FileServer                     active (pid = 23211, enabled)
Server:     Indexer-0                      active (pid = 23214, enabled)
Server:     MonitorServer                  inactive (disabled)
Server:     OMERO.Glacier2                 active (pid = 23218, enabled)
Server:     OMERO.IceStorm                 active (pid = 23219, enabled)
Server:     Processor-0                    active (pid = 23221, 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/omerouser/omero/omero_dist/var/log exists

Log files:  Blitz-0.log                    755.0 KB      errors=3    warnings=144
Log files:  DropBox.log                    5.0 KB        errors=14   warnings=0   
Log files:  FileServer.log                 2.0 KB       
Log files:  Indexer-0.log                  94.0 KB       errors=0    warnings=71 
Log files:  MonitorServer.log              6.0 KB        errors=7    warnings=0   
Log files:  OMEROweb-DEBUG.log             160.0 KB     
Log files:  OMEROweb.log                   65.0 KB       errors=25   warnings=0   
Log files:  Processor-0.log                10.0 KB       errors=0    warnings=2   
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                     1.10 MB

Parsing Blitz-0.log:[line:76] => Server restarted <=
Parsing Blitz-0.log:[line:302] => Server restarted <=
Parsing Blitz-0.log:[line:436] => Server restarted <=
Parsing Blitz-0.log:[line:2721] => Server restarted <=
Parsing Blitz-0.log:[line:3493] => Server restarted <=
Parsing Blitz-0.log:[line:3996] => Server restarted <=
Parsing Blitz-0.log:[line:4418] => Server restarted <=

Environment:OMERO_HOME=(unset)             
Environment:OMERO_NODE=(unset)             
Environment:OMERO_MASTER=(unset)           
Environment:PATH=/develop/software/java/jdk1.6.0_21/bin/:/develop/software/java/jdk1.6.0_21/bin/:/usr/kerberos/bin:/usr/local/bin:/usr/bin:/bin:/usr/X11R6/bin:/opt/ibm/db2/V9.7/bin:/usr/lib64/python2.3/site-packages/Ice/:/opt/ibm/db2/V9.7/bin:/usr/lib64/python2.3/site-packages/Ice/
Environment:ICE_HOME=(unset)               
Environment:LD_LIBRARY_PATH=:/usr/lib64/python2.3/site-packages/Ice/
Environment:DYLD_LIBRARY_PATH=(unset)     


I added LD_LIBRARY_PATH , and I couldn't still log in the web site...
I have no idea what's the problem...;;
It would be great any help, thanks in advance

Steve

Can you send us the var/log/OMEROweb*log files? Also, how did you configure and start OMERO.web? Thanks, ~Josh

I posted a log folder here.
I modified .bash_profile file to add 'LD_LIBRARY" path.
Then, I sourced the .bash_profile file.
command line) source .bash_profile
command line) ./omero web stop
command line) ./omero admin stop
command line) ./omero admin start
command line) ./omero web start

I still couldn't log in the omero site (localhost:4080/webadmin/login).
I tried all possible IDs and passwords related to omero. It doesn't work.

What's my problem ?
Do I need to set up web.configuration ? how I can execute this ?
I followed all instruction from the web site and it still doesn't work.

Do I need to install high version of rpm package ? ...
Any comments and suggestions will be great help to me !!

Thanks,
Steve

Hi Steve,

thanks for the logs. When you go to localhost:4080 do you see a login screen? From your OMEROweb-DEBUG.log, it looks like you have OMERO.web configured to use fastcgi-tcp. What this means is that when you run: 'bin/omero web start' it starts a process that waits on Apache or Nginx to talk to it. It doesn't talk to browsers directly.

For testing, you may want to switch this to the development server. As described under the "OMERO.web and Adminstration" section:

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$ bin/omero web stop # To stop the fastcgi-tcp process
$ bin/omero config set omero.web.application_server development
$ bin/omero web syncmedia
$ bin/omero web start


Now when you go to http://localhost:4080/webadmin, you should see the login page. If that doesn't work, please paste the output from the console here.

Thanks,
~Josh

Thanks for your reply.
I couldn't see the login page any more after I executed commands like as follows.

$ bin/omero web stop # To stop the fastcgi-tcp process
$ bin/omero config set omero.web.application_server development
$ bin/omero web syncmedia
$ bin/omero web start

also, error msg is like this.

Django version 1.1.1, using settings 'omeroweb.settings'
Development server is running at http://0.0.0.0:4080/
Quit the server with CONTROL-C.
Error: That port is already in use.

Now I could not open 'login page' any more.
I didn't have a problem to display a login main page before. only problem was that the system didn't allow me to login the web page. (I tried all possible passwords and IDs, but it seems not work)

anyway, is there anyway that I can log in the omero page ?
I stuck with this for a long time and still didn't know the solution.
Is there any guidance document that explains the whole installation process ?
(for cent os version)
I followed the step by step based on an omero web site manual. But, I still couldn't log in the page.
Seriously , we considered extending omero usages into a pathology image analysis domain.
Is there anyone who can help me fix this problem ?

Thanks,
Steve Oh

Hi Steve,

my guess is that from multiple attempts you now have background processes running, which we will eventually need to stop. I can help you finding them and stopping them via "ps" and "kill", or alternatively, you can configure a different port:

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bin/omero config set omero.web.application_server.port 9999
bin/omero web start


You should then see something like this:

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$ bin/omero web start
Starting OMERO.web...

Django version 1.1.1, using settings 'omeroweb.settings'
Development server is running at http://0.0.0.0:9999/
Quit the server with CONTROL-C.



At which point you can go to http://localhost:9999/webclient to login.

Cheers,
~Josh

Thanks for your reply.
I executed commands based on your comments like as follows.

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[omerouser@europa bin]$ ./omero web stop
Stopping OMERO.web... DEVELOPMENT: You will have to kill processes by hand!
[omerouser@europa bin]$ ./omero admin stop
Waiting on shutdown. Use CTRL-C to exit
.[omerouser@europa bin]$./omero config set omero.web.application_server.port 9999
[omerouser@europa bin]$ ./omero admin start
No descriptor given. Using etc/grid/default.xml
Waiting on startup. Use CTRL-C to exit
[omerouser@europa bin]$ ./omero web start
Starting OMERO.web... Validating models...
0 errors found

Django version 1.1.1, using settings 'omeroweb.settings'
Development server is running at http://0.0.0.0:9999/
Quit the server with CONTROL-C.
[04/Apr/2011 17:07:36] "GET /webclient HTTP/1.1" 301 0
[04/Apr/2011 17:07:36] "GET /webclient/ HTTP/1.1" 302 0
[04/Apr/2011 17:07:36] "GET /webclient/login/?url=/webclient/ HTTP/1.1" 200 2049
[04/Apr/2011 17:07:36] "GET /appmedia/omeroweb/css/layout.css HTTP/1.1" 200 6263
[04/Apr/2011 17:07:36] "GET /appmedia/omeroweb/css/login.css HTTP/1.1" 200 665
[04/Apr/2011 17:07:36] "GET /appmedia/omeroweb/images/logo-client.png HTTP/1.1" 200 27179
[04/Apr/2011 17:07:36] "GET /appmedia/omeroweb/images/ome.ico HTTP/1.1" 200 1406
[04/Apr/2011 17:24:54] "POST /webclient/login/?url=/webclient/ HTTP/1.1" 200 2239
[04/Apr/2011 17:25:16] "POST /webclient/login/?url=/webclient/ HTTP/1.1" 200 2235
[04/Apr/2011 17:25:34] "POST /webclient/login/?url=/webclient/ HTTP/1.1" 200 2244
[04/Apr/2011 17:25:52] "POST /webclient/login/?url=/webclient/ HTTP/1.1" 200 224


Then, I can see the login web page succesfully.
I tried all possible ID and passwords, but, I still couldn't log in the web site.
is there any way that I can add additional user to log in ? or
how I can change curret ID and password so that I may log in the web site ?

I attached login screen as a referece.
Also, it would be great help if you give me any advices.

Thanks,
Steve Oh

Hi Steve,

looks like we're making progress. Probably now the biggest issue is which user account to use where. You might want to read our Troubleshooting section on that topic before continuing.

In your screenshot, you are trying to login to OMERO.web with the user "omerouser". I notice from your console that this is your login account for Ubuntu ("omerouser@europa"). Unless you have knowingly created an OMERO user named "omerouser", then you won't be able to login. Instead, you'll want to login as "root", the sole administrative account in a new OMERO install.

If you have forgotten the root password (set during "bin/omero db script"), then you can reset it by running:

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bin/omero db password


and cut-n-pasting the output to "psql":

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$ bin/omero db password
Please enter password for OMERO root user:
Please re-enter password for OMERO root user:
UPDATE password SET hash = 'vvFwuczAmpyoRC0Nsv8FCw==' WHERE experimenter_id = 0;
$ psql YOURDBNAMEHERE -c "UPDATE password SET hash = 'vvFwuczAmpyoRC0Nsv8FCw==' WHERE experimenter_id = 0;"
UPDATE 1


Assuming you typed in "ome" as the response to "Please enter password for OMERO root user" above, then you'd log in to OMERO.web with "root" and "ome".

Hope that helps,
~Josh