Omero 5.1.2 ice35 "No processor available"

[remi_fr]

Dear all,

I am new to Omero and find it very nice and after an installation with which I had some issues I finally get it to work (almost).
I have a recurrent problem when exporting with Omero.figure, not all the time, but sometimes : "Unable to create figure, no processor available" I have read here that it is a known issue, I was wondering wether it had been fixed or not.
I also have some problems with some 'big' images that I have to treat. 5 stacks 5k x 5k, the projection picture would not display, and the Omero.figure tell me that it's too big... Is there any size limitations for pictures treatment in Omero ?
Of note I am currently running both server and insight on the same computer (that shouldn't be a problem I think). The server is a Mac pro 64Go RAM with 4 HD RAID 5 4.7 To and 2 processors quad core Xeon 2.4 GHz.

Also on Omero web, it doesn't seem to load the css, I guessed a permission problem of the folder where the css but that is not the case. I have attached a picture of my Omero.web webpage...

Here is the output of Omero diagnostics :

Code: Select all

================================================================================
OMERO Diagnostics 5.1.2-ice35
================================================================================
       
Commands:   java -version                  1.8.0     (/usr/bin/java)
Commands:   python -V                      2.7.10    (/usr/local/bin/python -- 2 others)
Commands:   icegridnode --version          3.5.1     (/usr/local/bin/icegridnode)
Commands:   icegridadmin --version         3.5.1     (/usr/local/bin/icegridadmin)
Commands:   psql --version                 9.4.4     (/usr/local/bin/psql)

Server:     icegridnode                    running
Server:     Blitz-0                        active (pid = 1323, enabled)
Server:     DropBox                        active (pid = 1325, enabled)
Server:     FileServer                     active (pid = 1324, enabled)
Server:     Indexer-0                      active (pid = 1326, enabled)
Server:     MonitorServer                  active (pid = 1327, enabled)
Server:     OMERO.Glacier2                 active (pid = 1328, enabled)
Server:     OMERO.IceStorm                 active (pid = 1331, enabled)
Server:     PixelData-0                    active (pid = 1329, enabled)
Server:     Processor-0                    active (pid = 1382, enabled)
Server:     Tables-0                       active (pid = 1454, enabled)
Server:     TestDropBox                    inactive (enabled)

Log dir:    /usr/local/Cellar/omero/5.1.2/var/log exists

Log files:  Blitz-0.log                    19.0 MB       errors=83   warnings=106
Log files:  DropBox.log                    6.0 KB        errors=8    warnings=3   
Log files:  FileServer.log                 1.0 KB       
Log files:  Indexer-0.log                  208.0 KB      errors=105  warnings=0   
Log files:  MonitorServer.log              2.0 KB        errors=2    warnings=0   
Log files:  OMEROweb.log                   8.0 KB        errors=6    warnings=6   
Log files:  OMEROweb_request.log           0.0 KB       
Log files:  PixelData-0.log                219.0 KB      errors=109  warnings=2   
Log files:  Processor-0.log                86.0 KB       errors=28   warnings=12 
Log files:  Tables-0.log                   58.0 KB       errors=34   warnings=12 
Log files:  TestDropBox.log                n/a
Log files:  master.err                     47.0 KB       errors=0    warnings=18 
Log files:  master.out                     0.0 KB       
Log files:  Total size                     20.02 MB


Environment:OMERO_HOME=(unset)             
Environment:OMERO_NODE=(unset)             
Environment:OMERO_MASTER=(unset)           
Environment:OMERO_USERDIR=(unset)         
Environment:OMERO_TMPDIR=(unset)           
Environment:PATH=/usr/local/bin:/usr/local/sbin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin
Environment:PYTHONPATH=(unset)             
Environment:ICE_HOME=(unset)               
Environment:LD_LIBRARY_PATH=(unset)       
Environment:DYLD_LIBRARY_PATH=(unset)     

OMERO SSL port:4064                           
OMERO TCP port:4063                           
OMERO data dir:'/Users/remi/var/OMERO.data'   Exists? True   Is writable? True
OMERO temp dir:'/Users/remi/omero/tmp'        Exists? True   Is writable? True   (Size: 0)

JVM settings: Blitz                         -Xmx7200m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Indexer                       -Xmx4800m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Pixeldata                     -Xmx7200m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Repository                    -Xmx4800m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions

OMERO.web status... [RUNNING] (PID 948)

If someone could have a look that would be very nice !

Thank you.

Remi

[manics]

Hi Remi

The diagnostics output shows there are some errors in the logs. Could you upload Your Blitz*.log and Processor*.log files? Either zip them up and attach them in a forum post, or upload them to https://www.openmicroscopy.org/qa2/qa/upload/

The CSS problem is usually due to restrictive permissions on the server or parent directories e.g. if it's in your home directory it may not be accessible by default. Your web server error logs should indicate if this is the problem. If you need more help can you post the generated web config and your web server logs?

Thanks, Simon

[remi_fr]

Hello and thanks for your answer,

The files have been uploaded but I'em not quite sure where...

the file is called logs.zip, don't know if you can retrieve them...

I'll have look at the folders permissions for the css problem.

Thanks let me know if I have to send the file again.

[cblackburn]

Hi Remi,

The zip file was uploaded okay. We'll take a look and get back to you shortly.

Cheers,

Colin

[remi_fr]

Thanks, I have just checked the permission :
the files are in :
/usr/local/Cellar/omero/5.1.2/lib/python/omeroweb/static/webgateway/css

All Folders are in "read only for everyone" permission, the only thing is that the owner is "system" for most of them.

Also the server is launched as an administrator (sudo) so the server should have the permission it needs to fetch the css or I haven't understood a thing with computers ?

[remi_fr]

short update :

The css files are accessible from my web browser directly, I can read them when accessing by their address, which seem to indicate that it's not a permission issue... here is my configuration file for nginx : (I'm not sure everything's right...). The 404 error (for example) are not logged into the file, whereas other server related errors notice or info are logged.

Code: Select all

#user  nobody;
worker_processes  1;

error_log /var/log/nginx/error.log;
error_log /var/log/nginx/error.log debug;
error_log /var/log/nginx/error.log  notice;
error_log /var/log/nginx/error.log  info;

#pid        logs/nginx.pid;


events {
    worker_connections 128 ;
}
http {

    sendfile on;
    send_timeout 60s;
    client_max_body_size 0;

        server {
        listen       8080;
        server_name  $hostname;

        sendfile on;
        client_max_body_size 0;

        # maintenance page serve from here
        location @maintenance {
            root /usr/local/Cellar/omero/5.1.2/etc/templates/error;
            try_files $uri /maintainance.html =502;
        }

        # weblitz django apps serve media from here
        location /static {
            alias /usr/local/Cellar/omero/5.1.2/lib/python/omeroweb/static;
        }

        location / {

            error_page 502 @maintenance;

            fastcgi_pass 127.0.0.1:4080;

            fastcgi_param PATH_INFO $fastcgi_script_name;


            fastcgi_param REQUEST_METHOD $request_method;
            fastcgi_param QUERY_STRING $query_string;
            fastcgi_param CONTENT_TYPE $content_type;
            fastcgi_param CONTENT_LENGTH $content_length;
            fastcgi_param SERVER_NAME $server_name;
            fastcgi_param SERVER_PROTOCOL $server_protocol;
            fastcgi_param SERVER_PORT $server_port;
            fastcgi_pass_header Authorization;
            fastcgi_intercept_errors on;
            fastcgi_read_timeout 60;
            # Uncomment if nginx SSL module is enabled or you are using nginx 1.1.11 or later
            # -- See: #10273, http://nginx.org/en/CHANGES
            # fastcgi_param HTTPS $https;
        }

    }


[atarkowska]

Hi Remi,

Could you please paste me the output of settings starting from omero.web.* when you do

Code: Select all

bin/omero config get

Please make sure you have the following:

Code: Select all

bin/omero config set omero.web.debug False
bin/omero config set omero.web.application_server "fastcgi-tcp"


Which command did you use to generate config: bin/omero web config nginx or nginx-development?

Could you try to stop web, delete /usr/local/Cellar/omero/5.1.2/lib/python/omeroweb/static folder and start again. What is the output when you started web

Code: Select all

bin/omero web start

From the nginx config I can see that you deployed OMERO.web on http://YOUR_HOST:8080/webclient. Could you confirm please as the screenshot doesn't say much about URL

What happen if you go to http://YOUR_HOST:8080/static/webclient/ ... in_web.png

Could you also check errors in your OMEROweb.log and nginx logfile /var/log/nginx/error.log? Alternatively please add more files to the page where you submitted first logs before QA 11311

Ola

[remi_fr]

Hi Ola,

here is what you asked for :
omero.data.dir=/Users/remi/var/OMERO.data
omero.db.name=omero_database
omero.db.pass=********
omero.db.user=remi
omero.web.application_server=fastcgi-tcp
omero.web.debug=False

omero web config nginx alone was the command I used

when deleting the folder and starting the web server again it copies all the files again...

Yes I used the port 8080 which shouldn't be a problem...

Well now I don't see the pictures so the address you gave me return an 404error

I'm sorry I didn't answer sooner I have been busy with other things :'(

Thanks a lot for your help anyway !

Rémi

[atarkowska]

Hi Remi,

when deleting the folder and starting the web server again it copies all the files again...

What was the output exactly? could you paste at least few lines from the very bottom including paths? Similar to:

Code: Select all

...
Copying '...js/ome.viewport.js'
Copying '...js/omero_image.js'
Post-processed 'omeroweb.viewer.min.css' as 'omeroweb.viewer.min.css'
Post-processed 'omeroweb.viewer.min.js' as 'omeroweb.viewer.min.js'

80 static files copied, 602 unmodified, 2 post-processed.
Clearing expired sessions. This may take some time...
[OK]
Starting OMERO.web... [OK]
$

Yes I used the port 8080 which shouldn't be a problem...

Well now I don't see the pictures so the address you gave me return an 404error

It is not clear to me how you could see the log on the login page (see screenshot above) if now you are saying that its url http://your_host:8080/static/webclient/ ... in_web.png gives you 404. Could you please be more specific, which URLs you are using? Please paste me the full URLs including real host and port. How the login page look exactly now? If logo is present could you run development tool, inspect element and copy the HTML including img src?

When you access the login page what exactly nginx error.log says? Could you include them as well?

Ola

[remi_fr]

here you go :

Code: Select all

art/img/icon-omero-insight.png'
Copying '/usr/local/Cellar/omero/5.1.2/lib/python/omeroweb/webstart/static/webstart/img/icon-omero-web.png'
Post-processed 'omeroweb.viewer.min.css' as 'omeroweb.viewer.min.css'
Post-processed 'omeroweb.viewer.min.js' as 'omeroweb.viewer.min.js'

375 static files copied, 2 post-processed.
Clearing expired sessions. This may take some time...
[OK]
Starting OMERO.web... [OK]
brs456-025:omeroweb remi$

here is the address : http://localhost:8080/webclient/login/? ... bclient%2F that's for the client, the page is returned with only one pic, i attach a screenshot.

as for the picture it is not present.
here is the image src : http://localhost:8080/static/webclient/ ... in_web.png which bring back a 404 error. the other one : (OME logo that displays fine is : http://localhost:8080/static/webgateway ... ey_110.png)

I attach the error log as well...

Thank you !

Rémi