Note
This documentation is for OMERO 5.2. This version is now in maintenance mode and will only be updated in the event of critical bugs or security concerns. OMERO 5.3 is expected in the first quarter of 2017.
Note
Since OMERO 5.2, the OMERO.web framework no longer bundles a copy of the Django package, instead manual installation of the Django dependency is required. It is highly recommended to use Django 1.8 (LTS) which requires Python 2.7. For more information see Python on the Version requirements page.
OMERO.web uses the Web Server Gateway Interface (WSGI) as a primary deployment platform. The Python standard PEP 3333 that describes how a web server communicates with web applications.
Install Django 1.8 and Gunicorn >= 19.3 using the package requirements file:
$ pip install -r share/web/requirements-py27-nginx.txt
Note
For more details refer to how to install Django 1.8 or upgrade Django to 1.8.
Additional settings can be configured by changing the following properties:
omero.web.wsgi_workers to (2 x NUM_CORES) + 1
Note
Do not scale the number of workers to the number of clients you expect to have. OMERO.web should only need 4-12 worker processes to handle many requests per second.
omero.web.wsgi_args Additional arguments. For more details check Gunicorn Documentation.
If you have installed Nginx, OMERO can automatically generate a configuration file for your web server. The location of the file will depend on your system, please refer to your web server’s manual. See Customizing your OMERO.web installation for additional customization options.
Set the following:
$ bin/omero config set omero.web.application_server "wsgi-tcp"
To create a site configuration file for inclusion in a system-wide nginx configuration redirect the output of the following command into a file:
$ bin/omero web config nginx
upstream omeroweb {
server 127.0.0.1:4080 fail_timeout=0;
}
server {
listen 80;
server_name $hostname;
sendfile on;
client_max_body_size 0;
# maintenance page serve from here
location @maintenance {
root /home/omero/OMERO.server/etc/templates/error;
try_files $uri /maintainance.html =502;
}
# weblitz django apps serve media from here
location /static {
alias /home/omero/OMERO.server/lib/python/omeroweb/static;
}
location @proxy_to_app {
proxy_set_header X-Forwarded-Proto $scheme;
proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
proxy_set_header Host $http_host;
proxy_redirect off;
proxy_buffering off;
proxy_pass http://omeroweb;
}
location / {
error_page 502 @maintenance;
# checks for static file, if not found proxy to app
try_files $uri @proxy_to_app;
}
}
Note
OMERO.web requires body_in_file_only adjusted in your default nginx config because nginx must buffer incoming data. Make sure you have that set to the following config:
http {
...
sendfile on;
send_timeout 60s;
client_max_body_size 0;
...
}
To configure an HTTPS server follow the nginx documentation.
Start the Gunicorn worker processes listening by default on 127.0.0.1:4080:
$ bin/omero web start
... static files copied to '/home/omero/OMERO.server/lib/python/omeroweb/static'.
Starting OMERO.web... [OK]
The Gunicorn workers are managed separately from other OMERO.server processes. You can check their status or stop them using the following commands:
$ bin/omero web status
OMERO.web status... [RUNNING] (PID 59217)
$ bin/omero web stop
Stopping OMERO.web... [OK]
Django WSGI workers (PID 59217) killed.
In order to offer users the ability to download data from OMERO.web you have to deploy using EXPERIMENTAL: Async workers. OMERO.web is able to handle multiple clients on a single worker thread switching context as necessary while streaming binary data from OMERO.server. Depending on the traffic and scale of the repository you should configure connections and speed limits on your server to avoid blocking resources. We recommend you run benchmark and performance tests. It is also possible to apply Download restrictions and offer alternative access to binary data.
Note
Handling streaming request/responses requires proxy buffering to be turned off. For more details refer to Gunicorn deployment and Nginx configuration.
Note
omero.web.application_server.max_requests should be set to 0
We run example benchmarks on rendering thumbnails and 512x512 pixels planes for 100 concurrent users making 5000 requests in total:
$ ab -n 5000 -c 100 https://server.openmicroscopy.org/omero/webclient/render_thumbnail/size/96/1234/
This is ApacheBench, Version 2.3 <$Revision: 1430300 $>
Copyright 1996 Adam Twiss, Zeus Technology Ltd, http://www.zeustech.net/
Licensed to The Apache Software Foundation, http://www.apache.org/
Server Software: nginx/1.9.9
Server Hostname: server.openmicroscopy.org
Server Port: 80
Document Path: /omero/webclient/render_thumbnail/size/96/31851/
Document Length: 1880 bytes
Concurrency Level: 100
Time taken for tests: 224.488 seconds
Complete requests: 5000
Failed requests: 0
Write errors: 0
Total transferred: 10450000 bytes
HTML transferred: 9400000 bytes
Requests per second: 22.27 [#/sec] (mean)
Time per request: 4489.763 [ms] (mean)
Time per request: 44.898 [ms] (mean, across all concurrent requests)
Transfer rate: 45.46 [Kbytes/sec] received
Connection Times (ms)
min mean[+/-sd] median max
Connect: 0 0 0.3 0 3
Processing: 435 4446 685.2 4363 7644
Waiting: 432 4446 685.3 4362 7644
Total: 435 4446 685.1 4363 7644
Percentage of the requests served within a certain time (ms)
50% 4363
66% 4553
75% 4670
80% 4750
90% 5072
95% 5398
98% 6795
99% 6955
100% 7644 (longest request)
$ ab -n 5000 -c 100 http://server.openmicroscopy.org/omero/webclient/render_image/1234/20/0/
This is ApacheBench, Version 2.3 <$Revision: 1430300 $>
Copyright 1996 Adam Twiss, Zeus Technology Ltd, http://www.zeustech.net/
Licensed to The Apache Software Foundation, http://www.apache.org/
Server Software: nginx/1.9.9
Server Hostname: server.openmicroscopy.org
Server Port: 80
Document Path: /omero/webclient/render_image/1234/20/0/
Document Length: 24293 bytes
Concurrency Level: 100
Time taken for tests: 247.154 seconds
Complete requests: 5000
Failed requests: 0
Write errors: 0
Total transferred: 122515000 bytes
HTML transferred: 121465000 bytes
Requests per second: 20.23 [#/sec] (mean)
Time per request: 4943.080 [ms] (mean)
Time per request: 49.431 [ms] (mean, across all concurrent requests)
Transfer rate: 484.09 [Kbytes/sec] received
Connection Times (ms)
min mean[+/-sd] median max
Connect: 0 0 0.4 0 4
Processing: 482 4898 855.3 4737 8303
Waiting: 476 4898 855.3 4737 8303
Total: 482 4898 855.2 4737 8303
Percentage of the requests served within a certain time (ms)
50% 4737
66% 5041
75% 5250
80% 5397
90% 5862
95% 6621
98% 7301
99% 8062
100% 8303 (longest request)
In order to identify why OMERO.web is not available run:
$ bin/omero web status
Then consult nginx error.log and OMERO.server/var/log/OMEROweb.log
For more details check OMERO.web issues.
To run the WSGI server in debug mode, enable Gunicorn logging using omero.web.wsgi_args:
$ bin/omero config set omero.web.wsgi_args -- "--log-level=DEBUG --error-logfile=/home/omero/OMERO.server/var/log/error.log".
Note
Experimental configurations are not ready for production use. Configuration may change. Features may not work properly.
OMERO.web deployment can be configured with sync and async workers. Sync workers are faster and recommended for a data repository with Download restrictions. If you wish to offer users the ability to download data then you have to use async workers; read more about Download limitations.
For more details refer to Gunicorn design.
Note
Experimental configurations are not ready for production use. Configuration may change. Features may not work properly.
Install futures
$ pip install futures
Additional settings can be configured by changing the following properties:
The number of worker threads for handling requests, see Gunicorn threads
$ bin/omero config set omero.web.wsgi_worker_class
$ bin/omero config set omero.web.wsgi_threads $(2-4 x NUM_CORES)
Note
Experimental configurations are not ready for production use. Configuration may change. Features may not work properly.
Install Gevent >= 0.13
$ pip install "gevent>=0.13"
Additional settings can be configured by changing the following properties:
The maximum number of simultaneous clients, see Gunicorn worker-connections
$ bin/omero config set omero.web.wsgi_worker_class gevent
$ bin/omero config set omero.web.wsgi_worker_connections 1000
$ bin/omero config set omero.web.application_server.max_requests 0