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Updated: Apr 6, 2021
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Useful when presenting. --- # What is uWSGI? - Python WSGI (Web Server Gateway Interface) application framework - Written in C - Forking application server - Optional HTTP server - Process manager ...and the rest of the kitchen sink ??? - What is uWSGI? - It's a framework for writting web applications. - uWSGI itself is written in C, but can run programs in different languages with a compatible interface. - It handles a lot of the scaling issues for us. --- # Why do we need uWSGI? - Galaxy is a Python web application without a web server - Implements standard Python WSGI - Some other application does the web serving - Technically we could use any HTTP/WSGI interface - Traditionally [Python Paste](https://github.com/cdent/paste/) ??? - We need uWSGI because Galaxy doesn't include a web server. - So Galaxy implements the standard Python WSGI interface. - And another application can handle the web serving. --- # What is uWSGI used for? .left[In a production Galaxy server:] - To start, manage, and scale web workers - Optionally, to start, manage, and scale job handlers ??? - Galaxy uses uWSGI to start, manage, and scale web workers. - Additionally it can be used for web-less job handlers if you use that setup. --- # Why uWSGI? Because Python can't multithread. ![Python GIL](../../images/gil.png) .footnote[Image credit: [Dariusz Fryta](http://www.tivix.com/blog/lets-go-python/)] ??? - Python cannot do multithreading due to the GIL or Global Interpreter Lock. - However, python is multiprocess capable. - uWSGI will provide our scalability. --- # Why uWSGI? - Fork many Galaxy server processes - Isolate job functions from web functions - Built in load balancing - Speak native high performance uWSGI protocol to nginx - Uninterrupted restarting - Can do anything you can imagine: [uWSGI configuration options](http://uwsgi-docs.readthedocs.io/en/latest/Options.html) ??? - uWSGI can fork as many Galaxy processes as we need. - Then it provides some built in load balancing with mules or zerg-mode. - It has a high-performance protocol that nginx and apache both speak, for more efficiency. - uWSGI enables uninterrupted restarts, which users love. --- ## uWSGI - **Configuration** - uWSGI wheel - Job handler mules ??? - There are three main sections we'll cover: Configuration, wheels, and mules. - First, configuration. --- ## uWSGI Configuration File uWSGI configuration is performed in the `uwsgi` key of `galaxy.yml`. `galaxy.yml.sample` is never consulted. .left[If using `run.sh`:] - If no config exists, all necessary defaults are generated as command line arguments to uWSGI - If a config exists, it is parsed, and any missing required options are passed as command line arguments to uWSGI **Galaxy servers deployed with Ansible do not use `run.sh` and should fully specify their uWSGI configuration.** ??? - uWSGI configuration is done in the uWSGI block of the galaxy yaml file. - The run shell script is not used in production, but has convenient behaviour for those users. --- ## uWSGI default command line Without a config file, the uWSGI command line is: ```sh-session $ /home/nate/galaxy/.venv/bin/python3 .venv/bin/uwsgi \ --module 'galaxy.webapps.galaxy.buildapp:uwsgi_app()' \ --virtualenv /home/nate/galaxy/.venv --pythonpath lib \ --threads 4 --http localhost:8080 \ --static-map /static=/home/nate/galaxy/static --die-on-term \ --hook-master-start 'unix_signal:2 gracefully_kill_them_all' \ --hook-master-start 'unix_signal:15 gracefully_kill_them_all' \ --enable-threads --py-call-osafterfork ``` ??? - The default uWSGI command line is quite complex with numerous arguments. - It must specify a module to load and a function to run. - A python path and virtualenv are loaded as well. - A number of threads is specified and an HTTP port on which to listen. - Static files required special mapping and some signal handling to ensure cleanup. --- ## uWSGI command line .left[Behind the scenes, `run.sh` calls `scripts/get_uwsgi_args.py`, which:] - locates your config file (if any), - parses it to determine whether you have set any of the default (or conflicting) options, - determines the flags needed to run Galaxy. You can take "full control" over this process by skipping `run.sh` and simply calling `uwsgi` directly, e.g. `uwsgi --yaml config/galaxy.yml`. ??? - If you're using run.sh, it calls a python script to determine the command line. - With Ansible this configuration is written in the galaxy yaml file. --- # uWSGI communication - uWSGI can serve HTTP directly using the `--http` option - uWSGI speaks a native protocol (which nginx also speaks) using `--socket` A proxy server is not *required,* but its use is strongly encouraged for performance reasons. ??? - uWSGI can speak either HTTP or it's own native protocol. - While a proxy server is not required, it is strongly encouraged. - It can use this more efficient uWSGI protocol and provide additional performance. - A proxy server can proxy static files, freeing uWSGI to focus on computation. --- ## YAML config uWSGI natively supports YAML configs (and INI, and PasteDeploy INI, and XML, and JSON, and ...) **WARNING:** "uWSGI YAML" is not real YAML! .pull-left[ Real YAML ```yaml uwsgi: # quoting forces string socket: '127.0.0.1:8001' # proper YAML list mule: - lib/galaxy/main.py - lib/galaxy/main.py ``` ] .pull-right[ uWSGI "YAML" ```yaml uwsgi: # quote chars read literally socket: '127.0.0.1:8001' # a uWSGI YAML "list": # repeat keys mule: lib/galaxy/main.py mule: lib/galaxy/main.py ``` ] ??? - uWSGI natively supports YAML configuration as well as a number of other formats. - However, uWSGI's YAML is not the same as real YAML. - It uses repeated keys for lists. --- ## YAML config - "uWSGI YAML" only applies to the `uwsgi` section of `galaxy.yml` - The `galaxy` section must use real YAML - uWSGI can be compiled against libyaml for real YAML support - Galaxy Ansible role can write *both* uWSGI (default), real YAML ??? - As a result of this uWSGI flavour of YAML, both are mixed in the Galaxy configuration file. - The Galaxy section must use proper YAML. - But not to worry! Ansible takes care of this dual-language configuration. - And you never have to worry about it. --- ## Configuration Schema .center[`[config_schema.yml][config-schema]` contains possible options **and their types**.] .left[config_schema.yml is the canonical source for config option documentation, from which:] - .left[`[galaxy.yml.sample][config-sample]` is generated] - [Galaxy configuration options documentation][config-docs] is generated [config-schema]: https://github.com/galaxyproject/galaxy/blob/release_20.09/lib/galaxy/webapps/galaxy/config_schema.yml [config-sample]: https://github.com/galaxyproject/galaxy/blob/release_20.09/lib/galaxy/config/sample/galaxy.yml.sample [config-docs]: https://docs.galaxyproject.org/en/master/admin/config.html ??? - Galaxy has a listing of every configuration option in the config_schema file. - This is used to generate the sample file and the documentation. --- ## uWSGI - Configuration - **uWSGI wheel** - Job handler mules ??? - The next main aspect of uWSGI is distribution, or wheels. --- ## uWSGI Wheel Galaxy's uWSGI is not built like standard `pip install uwsgi` A bit of technical minutiae that might help debugging ??? - Galaxy's uWSGI is not a standard package. - This is minutiae but it might help whenever you need to debug uWSGI issues. --- ## uWSGI Wheel - The challenge: - Unlike Galaxy's other framework dependencies, uWSGI is not a Python library - uWSGI embeds the CPython interpreter - Essentially uWSGI *is* Galaxy's CPython ??? - At the beginning we discussed it was a C program, uWSGI is not a python library. - So uWSGI embeds the CPython interpreter. -- - The goal: Provide a no-compilation-required, no-dependencies installation method for Galaxy that includes uWSGI that: - Doesn't embed statically linked CPython - Doesn't require system `libpythonX.Y.so` - Uses system CPython ??? - There are good reasons for this odd setup. - Our goal was to provide a compilation and dependency free method for installation. - Additionally it should not require system python libraries. --- ## uWSGI Wheel The uWSGI wheel is built differently than when built from source with `pip install uwsgi` - From source by pip: - Built as a single `uwsgi` ELF binary embedding the CPython interpreter - As the pyuwsgi wheel: - Built as a Python C extension into an ELF shared library `pyuwsgi.so` - Loaded by a stub `uwsgi` Python script by the CPython interpreter pyuwsgi wheel: the only way to precompile uWSGI in a way that does not require `libpythonX.Y.so` or ship CPython ??? - The uWSGI wheel is just built differently. - When it's built from source by pip, it comes as a single binary with CPython. - When it's usgin the wheel, it's built as a Python C extension. - This is loaded by a stub uWSGI script. - This complex method was the only one to achieve our goals. --- ## uWSGI - Configuration - uWSGI wheel - **Job handler mules** ??? - Lastly, we'll talk about job handling and mules. --- class: top ## Processes and Job Handling uWSGI starts up in a single "master" process and then `fork()`s a configured number of anonymous *web worker* processes to **serve web requests**. By default, web workers also handle Galaxy job (tool execution) preparation and completion. ??? - So how are processes and jobs handled with uWSGI? - uWSGI starts up in a single "master" process and forks some copies. - By default these also handle jobs. -- Processing Galaxy job (tool execution) preparation and finishing is somewhat resource intensive and affects web responsiveness. Production Galaxy servers traditionally start additional dedicated Galaxy "webless" (do not serve web requests) *job handler* processes. ??? - Processing galaxy jobs is quite resource intensive and can affect web responsiveness. - As a result, typically web handling and job handling are in separate processes. -- uWSGI provides a useful feature for running Galaxy job handlers: [uWSGI Mules](https://uwsgi-docs.readthedocs.io/en/latest/Mules.html). ??? - uWSGI has a feature called mules which we use for handlers. --- ## uWSGI Mules **Mules** are processes `fork()`ed from the uWSGI master after the application has been loaded and web workers have `fork()`ed. Mules can continue to run the same code or can load and run arbitrary code. Mules can receive messages from the web proceses. Mules can be pooled in to *Farms*, and messages can be sent to the farm to be handled by any mule in that farm. ??? - Mules are processes forked after the application has loaded. - Mules can continue to run the same code or load more. - Mules can communicate with the master. - Optionally they can live in pools called farms, e.g. one for job handlers. --- ## Mule Advantages .pull-left.reduce90[ Webless handlers - Config is complex - Must manage handler processes externally (e.g. w/ systemd) - Handler assignment: - At random from configured handlers - No regard as to handler health - Notification via database - Can be spread across multiple hosts ] .pull-right.reduce90[ uWSGI Mule handlers - Config is trivial - Handler processes managed automatically by uWSGI master - Handler assignment: - "Grabbed" by healthy mule - IPC (messaging) from web worker - Mules run on same host as web workers ] ??? - Webless handlers can be quite complex to setup and manage. - Mules offer a very simple alternative. - However, this requires they run on the same host, which is usually ok. --- ## Job Handler Mule Configuration Adding job handler mules is performed by simply instructing uWSGI to start them in `galaxy.yml`: ```yaml uwsgi: mule: lib/galaxy/main.py mule: lib/galaxy/main.py farm: job-handlers:1,2 ``` That's it! This Galaxy instance will now start and use two job handler mules. ??? - Mules can be defined by adding them to Galaxy's configuration in the uWSGI section. - Farms collect groups of mules. --- ## The full startup picture ??? - The full startup picture. --- class: top ## uWSGI Start/Run and Job Handling Lifecycle 1. Master process loads Galaxy application. ??? - We'll go quickly through the entire lifecycle of a Galaxy process. - First, the master uWSGI process loads Galaxy -- 2. Master `fork()`s web worker processes and begins serving web requests. ??? - This forks worker processes to serve web requests -- 3. Master `fork()`s job handler mules. ??? - Then mules are forked. -- 4. Mules reload Galaxy application as job handlers. ??? - Mules reload the application to behave as handlers. -- 5. The first mule to fully initialize grabs a lock on the farm message queue. ??? - The first mule ready establishes an exclusive lock on the queue -- 6. All additional mules wait on the lock. ??? - Additional mules wait and compete to access the queue. -- 7. A web worker receives a request for a new job. ??? - Next, a user visits Galaxy and submits a job. -- 8. The web worker creates a `job` record in the database but leaves the `handler` field `null`. ??? - The web worker creates a job in the database, but leaves it unassigned. -- 9. The web worker uses uWSGI's `farm_msg()` function to notify the `job-handlers` farm that a new job is ready to run. ??? - The worker pings the job handler farm that a new job is ready to run -- 10. The mule with the lock receives the message, assigns itself, and gives up the lock. ??? - The mule with the lock assigns itself and gives up the lock to go process the job. -- 11. Another mule acquires the lock and waits for the next message. ??? - Another mule acquires a lock and waits patiently. -- 12. Repeat ??? - This process repeats to process jobs. --- ## Advanced: Job Handler Assignment Methods **Mules can only be used if web workers and job handlers run on the same host.** The database can be used like a message queue to get the benefits of mules using webless job handlers. See [Job Handler Assignment Methods](https://docs.galaxyproject.org/en/master/admin/scaling.html#job-handler-assignment-methods) for details. Mules are preferred in scenarios where webless handlers are not needed. ??? - Mules are easy to setup, if you can run them on the same host. - This is usually the case. - If you have a more complex setup you might need webless job handlers. - There is documentation for when you need it. --- ## Advanced: Transparent Restart Provides uninterrupted restart capability (clients do not notice restarts). See [Transparent Restart](https://docs.galaxyproject.org/en/master/admin/scaling.html#transparent-restart-zerg-mode) and [uWSGI Zerg Mode documentation](https://uwsgi-docs.readthedocs.io/en/latest/Zerg.html) for details. ??? - Zerg mode (named after the game StarCraft) can be used for transparent restarts. - Users really like this, and it gives you freedom to make changes behind the scenes. --- ## Advanced: Zerg Mode + Job Handler Mules Combining both advanced modes was long thought to be impossible. However, a proof of concept has emerged! [Watch this space](https://gist.github.com/natefoo/6e45ae363ef434f38a935ff1b05b4b6e). ??? - Combining both was not thought to be possible but there is ongoing work. - A proof of concept exists, but it is not in any Ansible playbook yet. --- ## Thank you! This material is the result of a collaborative work. Thanks to the [Galaxy Training Network](https://training.galaxyproject.org) and all the contributors!
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