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Build Python 3 to statically link with libpython3.8.a for better performance

Summary

Python 3 traditionally in Fedora was built with a shared library libpython3.?.so and the final binary was dynamically linked against that shared library. This change is about creating the static library and linking the final python3 binary against it, as it provides significant performance improvement, up to 27% depending on the workload. The static library will not be shipped. The shared library will continue to exist in a separate subpackage. In essence, python3 will no longer depend on libpython.

Owner

Current status

  • Targeted release: Fedora 32
  • Last updated: 2019-10-31
  • Tracker bug: <will be assigned by the Wrangler>
  • Release notes tracker: <will be assigned by the Wrangler>

Detailed Description

When we compile the python3 package on Fedora (prior to this change), we create the libpython3.?.so shared library and the final python3 binary (/usr/bin/python3) is dynamically linked against it. However by building the libpython3.?.a static library and statically linking the final binary against it, we can achieve a performance gain of 5% to 27% depending on the workload. Link time optimizations and profile guided optimizations also have a greater impact when python3 is linked statically.

Since Python 3.8, C extensions must no longer be linked to libpython by default. Applications embedding Python now need to utilize the --embed flag for python3-config to be linked to libpython. During the Python 3.8 upgrade and rebuilds we've uncovered various cases of packages linking to libpython implicitly through various hacks within their buildsystems and fixed as many as possible. However, there are legitimate reasons to link an application to libpython and for those cases libpython should be provided so applications that embed Python can continue to do so.

This mirrors the Debian/Ubuntu way of building Python, where they offer a statically linked binary and an additional libpython subpackage. The libpython subpackage will be created and python3-devel will depend on it, so packages that embed Python will keep working.

The change was first done in Debian and Ubuntu years ago, followed by Python 3.8. manylinux1 and manylinux2010 ABI don't link C extensions to libpython either (to support Debian/Ubuntu).

By applying this change, libpython's namespace will be separated from Python's, so C extension which are still linked to libpython might experience side effects or break.

There is one exception for C extensions. If an application is linked to libpython in order to embed Python, C extensions used only within this application can continue to be linked to libpython.

Currently there is no upstream option to build the static library, as well as the shared one and statically link the final binary to it, so we have to rely on a downstream patch to achieve it. We plan to work with upstream to incorporate the changes there as well.

Before the change, python3.8 is dynamically linked to libpython3.8:

+-------------------+
|                   |
|                   |         +--------------------+
|  libpython3.8.so  <---------+ /usr/bin/python3.8 |
|                   |         +--------------------+
|                   |
+-------------------+

After the change, python3.8 is statically linked to libpython3.8:

                              +-----------------------+
                              |                       |
                              |   /usr/bin/python3.8  |
                              |                       |
+-------------------+         | +-------------------+ |
|                   |         | |                   | |
|                   |         | |                   | |
|  libpython3.8.so  |         | |  libpython3.8.a   | |
|                   |         | |                   | |
|                   |         | |                   | |
+-------------------+         | +-------------------+ |
                              +-----------------------+

As a negative side effect, when both libpython3.8.so and /usr/bin/python3.8 are installed, the filesystem footprint will be slightly increased (libpython3.8.so on Python 3.8.0, x86_64 is ~3.4M). OTOH only a very small amount of packages will depend on libpython3.8.so.

Benefit to Fedora

Python's performance will increase significantly depending on the workload. Since many core components of the OS also depend on Python this could lead to an increase in their performance as well, however individual benchmarks will need to be conducted to verify the performance gain for those components.

pyperformance results, ignoring differences smaller than 5%:

+-------------------------+------------------+------------------------------+
| Benchmark               | python38-3.8.0-1 | python38-3.8.0-666           |
+=========================+==================+==============================+
| nbody                   | 238 ms           | 174 ms: 1.36x faster (-27%)  |
+-------------------------+------------------+------------------------------+
| raytrace                | 919 ms           | 686 ms: 1.34x faster (-25%)  |
+-------------------------+------------------+------------------------------+
| scimark_lu              | 285 ms           | 215 ms: 1.33x faster (-25%)  |
+-------------------------+------------------+------------------------------+
| scimark_sparse_mat_mult | 8.20 ms          | 6.20 ms: 1.32x faster (-24%) |
+-------------------------+------------------+------------------------------+
| django_template         | 204 ms           | 156 ms: 1.31x faster (-24%)  |
+-------------------------+------------------+------------------------------+
| chaos                   | 203 ms           | 156 ms: 1.30x faster (-23%)  |
+-------------------------+------------------+------------------------------+
| logging_simple          | 15.6 us          | 12.2 us: 1.28x faster (-22%) |
+-------------------------+------------------+------------------------------+
| richards                | 124 ms           | 97.0 ms: 1.28x faster (-22%) |
+-------------------------+------------------+------------------------------+
| scimark_fft             | 652 ms           | 511 ms: 1.27x faster (-22%)  |
+-------------------------+------------------+------------------------------+
| hexiom                  | 17.4 ms          | 13.8 ms: 1.27x faster (-21%) |
+-------------------------+------------------+------------------------------+
| logging_format          | 17.1 us          | 13.5 us: 1.27x faster (-21%) |
+-------------------------+------------------+------------------------------+
| nqueens                 | 174 ms           | 137 ms: 1.26x faster (-21%)  |
+-------------------------+------------------+------------------------------+
| crypto_pyaes            | 201 ms           | 160 ms: 1.26x faster (-20%)  |
+-------------------------+------------------+------------------------------+
| deltablue               | 12.6 ms          | 10.0 ms: 1.25x faster (-20%) |
+-------------------------+------------------+------------------------------+
| unpickle_pure_python    | 576 us           | 463 us: 1.24x faster (-20%)  |
+-------------------------+------------------+------------------------------+
| pickle_pure_python      | 799 us           | 644 us: 1.24x faster (-19%)  |
+-------------------------+------------------+------------------------------+
| go                      | 449 ms           | 362 ms: 1.24x faster (-19%)  |
+-------------------------+------------------+------------------------------+
| spectral_norm           | 247 ms           | 200 ms: 1.24x faster (-19%)  |
+-------------------------+------------------+------------------------------+
| scimark_monte_carlo     | 185 ms           | 151 ms: 1.23x faster (-19%)  |
+-------------------------+------------------+------------------------------+
| logging_silent          | 340 ns           | 276 ns: 1.23x faster (-19%)  |
+-------------------------+------------------+------------------------------+
| unpickle                | 23.3 us          | 19.1 us: 1.22x faster (-18%) |
+-------------------------+------------------+------------------------------+
| float                   | 200 ms           | 166 ms: 1.21x faster (-17%)  |
+-------------------------+------------------+------------------------------+
| mako                    | 26.6 ms          | 22.0 ms: 1.21x faster (-17%) |
+-------------------------+------------------+------------------------------+
| xml_etree_generate      | 159 ms           | 133 ms: 1.20x faster (-17%)  |
+-------------------------+------------------+------------------------------+
| xml_etree_process       | 128 ms           | 107 ms: 1.20x faster (-16%)  |
+-------------------------+------------------+------------------------------+
| fannkuch                | 795 ms           | 670 ms: 1.19x faster (-16%)  |
+-------------------------+------------------+------------------------------+
| chameleon               | 15.7 ms          | 13.3 ms: 1.18x faster (-15%) |
+-------------------------+------------------+------------------------------+
| scimark_sor             | 347 ms           | 294 ms: 1.18x faster (-15%)  |
+-------------------------+------------------+------------------------------+
| pathlib                 | 35.7 ms          | 30.2 ms: 1.18x faster (-15%) |
+-------------------------+------------------+------------------------------+
| regex_compile           | 301 ms           | 255 ms: 1.18x faster (-15%)  |
+-------------------------+------------------+------------------------------+
| genshi_text             | 48.3 ms          | 41.2 ms: 1.17x faster (-15%) |
+-------------------------+------------------+------------------------------+
| sympy_str               | 459 ms           | 394 ms: 1.17x faster (-14%)  |
+-------------------------+------------------+------------------------------+
| genshi_xml              | 102 ms           | 87.6 ms: 1.16x faster (-14%) |
+-------------------------+------------------+------------------------------+
| 2to3                    | 540 ms           | 465 ms: 1.16x faster (-14%)  |
+-------------------------+------------------+------------------------------+
| sqlite_synth            | 4.89 us          | 4.25 us: 1.15x faster (-13%) |
+-------------------------+------------------+------------------------------+
| sympy_expand            | 704 ms           | 613 ms: 1.15x faster (-13%)  |
+-------------------------+------------------+------------------------------+
| html5lib                | 162 ms           | 141 ms: 1.15x faster (-13%)  |
+-------------------------+------------------+------------------------------+
| sympy_integrate         | 34.2 ms          | 30.0 ms: 1.14x faster (-12%) |
+-------------------------+------------------+------------------------------+
| dulwich_log             | 121 ms           | 107 ms: 1.13x faster (-11%)  |
+-------------------------+------------------+------------------------------+
| sympy_sum               | 286 ms           | 253 ms: 1.13x faster (-11%)  |
+-------------------------+------------------+------------------------------+
| xml_etree_iterparse     | 170 ms           | 152 ms: 1.12x faster (-11%)  |
+-------------------------+------------------+------------------------------+
| telco                   | 10.2 ms          | 9.14 ms: 1.11x faster (-10%) |
+-------------------------+------------------+------------------------------+
| meteor_contest          | 171 ms           | 154 ms: 1.11x faster (-10%)  |
+-------------------------+------------------+------------------------------+
| json_dumps              | 20.0 ms          | 18.0 ms: 1.11x faster (-10%) |
+-------------------------+------------------+------------------------------+
| tornado_http            | 425 ms           | 384 ms: 1.11x faster (-10%)  |
+-------------------------+------------------+------------------------------+
| xml_etree_parse         | 249 ms           | 226 ms: 1.10x faster (-9%)   |
+-------------------------+------------------+------------------------------+
| sqlalchemy_imperative   | 53.4 ms          | 49.6 ms: 1.08x faster (-7%)  |
+-------------------------+------------------+------------------------------+
| python_startup          | 13.7 ms          | 12.7 ms: 1.07x faster (-7%)  |
+-------------------------+------------------+------------------------------+
| json_loads              | 43.3 us          | 40.7 us: 1.06x faster (-6%)  |
+-------------------------+------------------+------------------------------+
| python_startup_no_site  | 9.29 ms          | 8.75 ms: 1.06x faster (-6%)  |
+-------------------------+------------------+------------------------------+
| pickle_dict             | 33.8 us          | 32.0 us: 1.06x faster (-5%)  |
+-------------------------+------------------+------------------------------+
| sqlalchemy_declarative  | 272 ms           | 258 ms: 1.05x faster (-5%)   |
+-------------------------+------------------+------------------------------+

Scope

  • Proposal owners:
    • Review and merge the pull request with the implementation.
    • Go through the Python C extension packages that are linked to libpython and test if things work correctly. A copr repository will be provided for testing.
  • Other developers: Other developers are encouraged to test the new statically linked python3 and check if their package works as expected
  • Release engineering: #8953 This change does not require a mass rebuild, however a rebuild of the affected packages will be required. The affected packages will be rebuilt in copr first.
  • Policies and guidelines: The packaging guidelines will need to be updated to explicitly mention that C extensions should not be linked to libpython, and that the python3 binary is statically linked.
  • Trademark approval: N/A (not needed for this Change)

Upgrade/compatibility impact

Affected package maintainers should verify that their packages work as expected and the only impact the end users should see is a performance increase for workloads relying on Python.

How To Test

Copr repo with instructions: https://copr.fedorainfracloud.org/coprs/g/python/Python3_statically_linked/

Package changes test

The change will bring the new libpython3 subpackage as a dependency of python3-devel.

Test that it's installed:

$ rpm -q libpython3

Test that it's uninstalled if python3-devel is removed:

$ dnf remove python3-devel

Test that python3-libs no longer includes the libpython shared library.

$ rpm -ql python3-libs | grep libpython3

Dynamic linker test

To check that the python3.8 program is not linked to libpython, ldd can be used. For example, Python 3.7 will still be linked to libpython:

$ ldd /usr/bin/python3.7|grep libpython
libpython3.7m.so.1.0 => /lib64/libpython3.7m.so.1.0 (0x00007fbb57333000)

But python3.8 will no longer be linked to libpython:

$ ldd /usr/bin/python3.8|grep libpython

Performance test

The performance speedup can be measured using the official Python benchmark suite pyperformance: see Run benchmarks.

Namespace test

The following script can be used to verify that the change is in effect:

import ctypes
import sys
 
EMPTY_TUPLE_SINGLETON = ()

def get_empty_tuple(lib):
    # Call PyTuple_New(0)
    func = lib.PyTuple_New
    func.argtypes = (ctypes.c_ssize_t,)
    func.restype = ctypes.py_object
    return func(0)
 
def test_lib(libname, lib):
    obj = get_empty_tuple(lib)
    if obj is EMPTY_TUPLE_SINGLETON:
        print("%s: SAME namespace" % libname)
    else:
        print("%s: DIFFERENT namespace" % libname)

def test():
    program = ctypes.pythonapi

    if hasattr(sys, 'abiflags'):
        abiflags = sys.abiflags
    else:
        # Python 2
        abiflags = ''
    ver = sys.version_info
    filename = ('libpython%s.%s%s.so.1.0'
                % (ver.major, ver.minor, abiflags))
    libpython = ctypes.cdll.LoadLibrary(filename)

    test_lib('program', program)
    test_lib('libpython', libpython)

test()

Output before the change:

program: SAME namespace
libpython: SAME namespace

Output after the change:

program: SAME namespace
libpython: DIFFERENT namespace

User Experience

Python based workloads should see a performance gain of up to 27%.

Dependencies

While this specific change is not dependent on anything else, we would like to ensure that all the packages that link to libpython continue to work as expected.

Currently (30/10/2019) 118 packages on rawhide depend on libpython.

Result of the "repoquery --repo=rawhide --source --whatrequires 'libpython3.8.so.1.0()(64bit)' " command on Fedora Rawhide, x86_64:

  • COPASI
  • Io-language
  • OpenImageIO
  • YafaRay
  • antimony
  • blender
  • boost
  • calamares
  • calibre
  • cantor
  • ceph
  • clingo
  • condor
  • createrepo_c
  • csound
  • cvc4
  • dionaea
  • dmlite
  • domoticz
  • fontforge
  • freecad
  • gdb
  • gdcm
  • gdl
  • getdp
  • glade
  • globus-net-manager
  • glom
  • gnucash
  • gpaw
  • hamlib
  • hokuyoaist
  • hugin
  • insight
  • kdevelop-python
  • kicad
  • kitty
  • krita
  • lammps
  • ldns
  • libCombine
  • libarcus
  • libarcus-lulzbot
  • libbatch
  • libcec
  • libcomps
  • libdnf
  • libftdi
  • libkml
  • libkolabxml
  • libldb
  • libnuml
  • libpeas
  • libplist
  • libreoffice
  • librepo
  • libsavitar
  • libsbml
  • libsedml
  • libtalloc
  • libyang
  • libyui-bindings
  • link-grammar
  • lldb
  • mathgl
  • med
  • mod_wsgi
  • nautilus-python
  • nbdkit
  • nest
  • netgen-mesher
  • neuron
  • nextpnr
  • nordugrid-arc
  • nwchem
  • openbabel
  • openscap
  • opentrep
  • openvdb
  • pam_wrapper
  • paraview
  • perl-Inline-Python
  • pidgin
  • pitivi
  • plplot
  • postgresql
  • pynac
  • pyotherside
  • pythia8
  • python
  • python-gstreamer1
  • python-jep
  • python-qt5
  • python3
  • qgis
  • qpid-dispatch
  • qpid-proton
  • rdkit
  • renderdoc
  • rmol
  • root
  • samba
  • scidavis
  • sigil
  • swift-lang
  • texworks
  • thunarx-python
  • trademgen
  • trellis
  • unbound
  • uwsgi
  • vdr-epg-daemon
  • vigra
  • vim
  • vrpn
  • vtk
  • weechat
  • znc

Contingency Plan

  • Contingency mechanism: If issues appear that cannot be fixed in a timely manner the change can be easily reverted and will be considered again for the next fedora release. Also a proper upgrade path mechanism will be provided in case of reversion, since libpython.3.?.so will be a separate package with this change.
  • Contingency deadline: Before the beta freeze of Fedora 32 (2020-02-25)
  • Blocks release? Yes
  • Blocks product? None

Documentation

The documentation will be reflected in the changes for the python packaging guidelines.

Release Notes