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Python: Optional Bytecode Cache

Summary

The Python standard library bytecode cache files (e.g. /usr/lib64/python3.9/.../__pycache__/*.pyc) will be moved from the python3-libs package to three new optional subpackages (split by optimization level). The non-optimized bytecode cache will be recommended by python3-libs and installed by default but removable. The bytecode cache optimization level 1 and 2 will not be recommended (and hence will not be installed by default) but will be installable. The default SELinux policy will be adapted not to audit AVC denials when the bytecode cache is created by Python on runtime. This will save 8.89 MiB disk space on default installations or 17.12 MiB on minimal installations (by opting-out from the recommended subpackage with non-optimized bytecode cache). When all three new packages are installed, the size will increase slightly over the status quo (by 4.5 MiB).

Owner

Current status

  • Targeted release: Fedora 34
  • Last updated: 2020-09-08
  • FESCo issue: <will be assigned by the Wrangler>
  • Tracker bug: <will be assigned by the Wrangler>
  • Release notes tracker: <will be assigned by the Wrangler>

Detailed Description

What is the Python bytecode cache

When Python code is interpreted, it is compiled to Python bytecode. When a pure Python module is imported for the first time, the compiled bytecode is serialized and cached to a .pyc file located in the __pycache__ directory next to the .py source. Subsequent imports use the cache directly, until it is invalidated (for example when the .py source is edited and its mtime stamp is bumped) -- at that point, the cache is updated. This behavior is explained in detail in PEP 3147. The invalidation is described in PEP 552.

Python can operate in 3 different optimization levels: 0, 1 and 2. By default, the optimization level is 0. When invoked with the -O command line option optimization is set to 1, similarly with -OO it is 2. Bytecode cache for different optimization levels is saved with different filenames as described in PEP 488.

As an example, a Python module located at /path/to/basename.py will have bytecode cache files for CPython 3.9 stored as:

  • /path/to/__pycache__/basename.cpython-39.pyc for the non-optimized bytecode
  • /path/to/__pycache__/basename.cpython-39.opt-1.pyc for optimization level 1
  • /path/to/__pycache__/basename.cpython-39.opt-2.pyc for optimization level 2

Python bytecode cache in RPM packages (status quo)

Pure Python modules shipped in RPM packages (and namely the ones shipped trough the python3-libs package) are located at paths not writable by regular user, under /usr/lib(64)/python3.9/, hence the bytecode cache is also located in such locations. To work around this problem, the bytecode cache is pre-compiled when RPM packages are built and python3-libs ships and owns the sources as well as the bytecode cache: 

$ rpm -ql python3-libs
...
/usr/lib64/python3.9/__pycache__/ast.cpython-39.opt-1.pyc
/usr/lib64/python3.9/__pycache__/ast.cpython-39.opt-2.pyc
/usr/lib64/python3.9/__pycache__/ast.cpython-39.pyc
...
/usr/lib64/python3.9/ast.py
...

As a result, the package is quite big, essentially shipping all pure Python modules 4 times.

Depending of the module content, its bytecode cache files might be identical across optimization levels. For such cases, the files are hardlinked to reduce the bloat: 

$ ls -1i /usr/lib64/python3.9/collections/__pycache__/abc.*pyc
8634 /usr/lib64/python3.9/collections/__pycache__/abc.cpython-39.opt-1.pyc
8634 /usr/lib64/python3.9/collections/__pycache__/abc.cpython-39.opt-2.pyc
8634 /usr/lib64/python3.9/collections/__pycache__/abc.cpython-39.pyc

This is however not possible for all the modules from python3-libs: 

$ ls -1i /usr/lib64/python3.9/__pycache__/ast.*pyc
8438 /usr/lib64/python3.9/__pycache__/ast.cpython-39.opt-1.pyc
8440 /usr/lib64/python3.9/__pycache__/ast.cpython-39.opt-2.pyc
8441 /usr/lib64/python3.9/__pycache__/ast.cpython-39.pyc

What if the bytecode cache would not be packaged

When the bytecode cache is not packaged, several things happen:

  1. When non-root users run Python, the imported modules are never cached. As a result, the startup time of Python apps might be slightly larger than necessary until root runs them.
  2. When root runs Python, the imported modules are cached. As a result untracked .pyc files start to pop up in /usr/lib(64)/python3.9/. When the system is updated to a newer Python version, the untracked files remain on the filesystem until manually cleaned up.
  3. When root runs Python in SELinux restricted context, the imported modules are attempted to be cached but SELinux does not allow that. The result is same as (1) with a lot of noise from SELinux.

Packaging the bytecode cache into optional subpackages

To be able to save quite some disk space without disrupting the user experience, we propose to ship the pre-compiled bytecode cache previously included in python3-libs as follows:

In order to properly own any runtime-generated bytecode-cache files, the python3-libs will list all files listed in the three abovementioned packages as %ghost.

python3-libs will not Require any of the bytecode cache packages, hence the packages will be (un)installable and fully optional.

Given that almost all Fedora Python packages invoke Python in the non-optimized mode¹, python3-libs will Recommend python3-libs-bytecode-opt-0 and hence the package will be installed by default together with Python; the user experience will remain the same for the vast majority of users and use cases.

Furthermore, container images and other minimal systems maintainers may choose to exclude the python3-libs-bytecode-opt-0 package to save more disk space if desired.

Note that by splitting the three optimization levels to different RPM packages, files can no longer be hardlinked between each other. This results in a slight size increase when all three optimization levels are installed. The change owners consider the need for all three subpackages to be present simultaneously on one size-sensitive system unlikely and hence consider this a fair trade.

¹ No real data was collected to support this claim. This hypothesis is made by the Python maintainers based on their own experience.

SELinux policy changes

In order to suppress the otherwise omnipresent AVC denial messages about Python failing to write the bytecode cache, the Python maintainers have teamed up with the Fedora's selinux-policy maintainers to suppress those. The implementation details about this are available at:

When Python runs under the root user in SELinux restricted context, SELinux will still prevent it from writing the bytecode cache, but it will not clutter the audit log.

Size impact

Sizes calculated in mock on x86_64. Only python3-libs and the relevant bytecode cache packages were installed (i.e. no other Python packages). By du -c /usr/lib64/python3.9 (converted to MiBs by dividing by 1024 and rounding to 2 decimal places).

Situation Size of /usr/lib(64)/python3.9 Difference in MiB Difference in %
Status quo (before this change) 31.84 MiB
Default (non-optimized cache only) 22.96 MiB -8.89 MiB -27.91 %
No cache 14.72 MiB -17.12 MiB -53.77 %
Levels 0 and 1 29.71 MiB -2.13 MiB -6.70 %
All optimization levels (like before) 36.35 MiB +4.50 MiB +14.14 %

Speed impact

The presence or absence of the bytecode cache only impacts the speed of imports. It is most common that the imports happen while an application starts. Once the application is running, there is no speed difference.

A totally inappropriate and unscientific experiment: 

$ du -a /usr/lib64/python3.9/ | grep py$ | sort -n -r | head -n 1
224	/usr/lib64/python3.9/_pydecimal.py

With caches: 

$ time python3 -c 'import importlib as i, _pydecimal as p; [i.reload(p) for _ in range(10000)]'

real	0m13.986s
user	0m13.554s
sys	0m0.365s

$ time python3 -O -c 'import importlib as i, _pydecimal as p; [i.reload(p) for _ in range(10000)]'

real	0m13.594s
user	0m13.186s
sys	0m0.337s

$ time python3 -OO -c 'import importlib as i, _pydecimal as p; [i.reload(p) for _ in range(10000)]'

real	0m13.225s
user	0m12.855s
sys	0m0.290s


Without caches: 

$ time python3 -c 'import importlib as i, _pydecimal as p; [i.reload(p) for _ in range(10000)]'

real	4m20.554s
user	4m14.600s
sys	0m4.850s

$ time python3 -O -c 'import importlib as i, _pydecimal as p; [i.reload(p) for _ in range(10000)]'

real	4m14.291s
user	4m9.333s
sys	0m3.721s

$ time python3 -OO -c 'import importlib as i, _pydecimal as p; [i.reload(p) for _ in range(10000)]'

real	4m14.816s
user	4m11.035s
sys	0m2.400s

This suggests that an application that does 10000 module imports (with rather large 224 KiB modules) would be slowed down on start by 4 minutes. Obviously, such measurements depend on many aspects and doing 10000 imports is rather far-fetched -- there are only ~550 pure Python modules in python3-libs, hence even if they all are imported, the slowdown should not exceed couple seconds. However, it is indisputable that importing modules without the cache is significantly slower.

Deployments negatively impacted by this are advised to either install the appropriate bytecode subpackage or pre-compile the relevant modules ahead of time (e.g. when building a container image).

Rejected ideas

In this section, we briefly describe ideas that were presented by others or considered by the change owners, but rejected.

Many Python minimization proposals were previously described in great detail in Python minimization in Fedora and discussed on the devel mailing list.

Stop shipping mandatory .py sources, ship only .pyc cache

This is described as Solution 7 in the abovementioned document.

It is possible to ship bytecode cache installed e.g. as /usr/lib64/python3.9/ast.pyc instead of the appropriate Python source (e.g. /usr/lib64/python3.9/ast.py in our example). Such solution could save additional 3.1 MiB when no sources and no other optimization levels would be shipped. In addition, it would also not suffer from any import slowdowns regardless of the optimization level Python was invoked with. Our analysis however shows significant drawbacks when shipping .pyc files only:

  • Without the source codes, some Python tracebacks are less informational.
  • Without the source codes, many IDEs and other Python developer tools might be confused (e.g. code completion or the IPython ?? syntax to show a function's code).
  • Sysadmins and ops are notoriously known to edit Python source files (including the standard library) on production 🎩.
  • The shipped .pyc files would need to be compiled with a certain optimization level (presumably 0, without loss of generality). Python invoked with -O or -OO would still execute such .pyc file regardless -- in special circumstances, this can lead to slight behavior nuances that would be very hard to debug.

This can be somehow worked around by offering the possibility to install the sources (or even recommend them by default). However:

  • With module.py present, the module.pyc files is always totally ignored.
  • The module.py would then still need to ship various optimization level bytecode caches in the __pycache__ directory, possibly duplicating module.pyc and __pycache__/module.cpython-39.pyc (there is no way to hardlink those on RPM level, since they are in different directory).
  • Just by installing the optional sources on production in order to be able to debug problems, Python invoked in different optimization level than the one used to pre-compile the shipped module.pyc would suddenly start executing different bytecode, essentially producing a haisenbug waiting to happen.

The change owners consider shipping individual well-tested, large, modules with machine-generated sources as .pyc only to save space a reasonable compromise (and it was already done with pydoc_data.topics and several encodings submodules). However doing it with the entire standard library would provide a very non-standard user experience and might possibly blow up at many places.

Make Python not attempt to write bytecode cache into /usr/lib(64)/python3.9

Originally, when panning this change, the idea was to prevent Python to write the bytecode cache to /usr/lib(64)/python3.9/... on imports by a special marker file (e.g. /usr/lib(64)/python3.9/nocache or similar). Such marker would mean "this directory (possibly recursively) contains bytecode maintained by non-Python tooling". Python would use the cache if present, but it would not even attempt to write the cache if it is missing or outdated. Such change of behavior would need to be introduced in Python upstream.

When drafting this change for upstream, we have failed to provide sufficient reasoning to introduce such new behavior. The only problems with writing the cache identified by the change owners were:

  • files not owned by any RPM package (solved by %ghost)
  • SELinux AVC denials noise (solved by adapting selinux-policy)

Hence, this idea was rejected.

Keep the hardlink based filesize optimizations by RPM trickery

When all three bytecode packages are installed, the disk usage is slightly bigger than before this change because files in different packages cannot be hardlinked on RPM level. In theory, it might be possible to compensate this by various means. For example:

  • Hardlink the files in %posttrans scriplet.
  • On build time, detect what files are identical, hardlink such files and include all their instances in all relevant packages (e.g. all three bytecode packages would contain all three hardlinked versions of __pycache__/abc.cpython-39*.pyc, but only one version of __pycache__/ast.cpython-39*.pyc).

Such solutions are considered not worth it by the change owners, because they would make the user experience and/or the packaging unnecessary complicated. As said previously, the change owners consider the need for all three subpackages to be present simultaneously on one size-sensitive system unlikely.

Not realized ideas

In this section, we briefly describe ideas that were presented by others or considered by the change owners, but were not realized (e.g. for capacity reasons). Such ideas may be realized later.

Store bytecode cache in /var/cache and/or ~/.cache

Apply this change to all Python RPM packages

Feedback

Benefit to Fedora

Scope

  • Other developers: N/A (not a System Wide Change)
  • Release engineering: N/A (not a System Wide Change)
  • Policies and guidelines: N/A (not a System Wide Change)
  • Trademark approval: N/A (not needed for this Change)

Upgrade/compatibility impact

N/A (not a System Wide Change)

How To Test

N/A (not a System Wide Change)

User Experience

Dependencies

N/A (not a System Wide Change)

Contingency Plan

  • Contingency mechanism: (What to do? Who will do it?) N/A (not a System Wide Change)
  • Contingency deadline: N/A (not a System Wide Change)
  • Blocks release? N/A (not a System Wide Change), Yes/No
  • Blocks product? product

Documentation

N/A (not a System Wide Change)

Release Notes

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