I took a close look at how Debian builds the Python interpreter,
because I noticed it ran substantially faster than the one in nixpkgs
and I was curious why.
One thing that I found made a material difference in performance was
this pair of linker flags (passed to the compiler):
-Wl,-O1 -Wl,-Bsymbolic-functions
In other words, effectively the linker gets passed the flags:
-O1 -Bsymbolic-functions
Doing the same thing in nixpkgs turns out to make the interpreter
run about 6% faster, which is quite a big win for such an easy
change. So, let's apply it.
---
I had not known there was a `-O1` flag for the *linker*!
But indeed there is.
These flags are unrelated to "link-time optimization" (LTO), despite
the latter's name. LTO means doing classic compiler optimizations
on the actual code, at the linking step when it becomes possible to
do them with cross-object-file information. These two flags, by
contrast, cause the linker to make certain optimizations within the
scope of its job as the linker.
Documentation is here, though sparse:
https://sourceware.org/binutils/docs-2.31/ld/Options.html
The meaning of -O1 was explained in more detail in this LWN article:
https://lwn.net/Articles/192624/
Apparently it makes the resulting symbol table use a bigger hash
table, so the load factor is smaller and lookups are faster. Cool.
As for -Bsymbolic-functions, the documentation indicates that it's a
way of saving lookups through the symbol table entirely. There can
apparently be situations where it changes the behavior of a program,
specifically if the program relies on linker tricks to provide
customization features:
https://bugs.launchpad.net/ubuntu/+source/xfe/+bug/644645https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=637184#35
But I'm pretty sure CPython doesn't permit that kind of trick: you
don't load a shared object that tries to redefine some symbol found
in the interpreter core.
The stronger reason I'm confident using -Bsymbolic-functions is
safe, though, is empirical. Both Debian and Ubuntu have been
shipping a Python built this way since forever -- it was introduced
for the Python 2.4 and 2.5 in Ubuntu "hardy", and Debian "lenny",
released in 2008 and 2009. In those 12 years they haven't seen a
need to drop this flag; and I've been unable to locate any reports
of trouble related to it, either on the Web in general or on the
Debian bug tracker. (There are reports of a handful of other
programs breaking with it, but not Python/CPython.) So that seems
like about as thorough testing as one could hope for.
---
As for the performance impact: I ran CPython upstream's preferred
benchmark suite, "pyperformance", in the same way as described in
the previous commit. On top of that commit's change, the results
across the 60 benchmarks in the suite are:
The median is 6% faster.
The middle half (aka interquartile range) is from 4% to 8% faster.
Out of 60 benchmarks, 3 come out slower, by 1-4%. At the other end,
5 are at least 10% faster, and one is 17% faster.
So, that's quite a material speedup! I don't know how big the
effect of these flags is for other software; but certainly CPython
tends to do plenty of dynamic linking, as that's how it loads
extension modules, which are ubiquitous in the stdlib as well as
popular third-party libraries. So perhaps that helps explain why
optimizing the dynamic linker has such an impact.
Without this flag, the configure script prints a warning at the end,
like this (reformatted):
If you want a release build with all stable optimizations active
(PGO, etc), please run ./configure --enable-optimizations
We're doing a build to distribute to people for day-to-day use,
doing things other than developing the Python interpreter. So
that's certainly a release build -- we're the target audience for
this recommendation.
---
And, trying it out, upstream isn't kidding! I ran the standard
benchmark suite that the CPython developers use for performance
work, "pyperformance". Following its usage instructions:
https://pyperformance.readthedocs.io/usage.html
I ran the whole suite, like so:
$ nix-shell -p ./result."$variant" --run '
cd $(mktemp -d); python -m venv venv; . venv/bin/activate
pip install pyperformance
pyperformance run -o ~/tmp/result.'"$variant"'.json
'
and then examined the results with commands like:
$ python -m pyperf compare_to --table -G \
~/tmp/result.{$before,$after}.json
Across all the benchmarks in the suite, the median speedup was 16%.
(Meaning 1.16x faster; 14% less time).
The middle half of them ranged from a 13% to a 22% speedup.
Each of the 60 benchmarks in the suite got faster, by speedups
ranging from 3% to 53%.
---
One reason this isn't just the default to begin with is that, until
recently, it made the build a lot slower. What it does is turn on
profile-guided optimization, which means first build for profiling,
then run some task to get a profile, then build again using the
profile. And, short of further customization, the task it would use
would be nearly the full test suite, which includes a lot of
expensive and slow tests, and can easily take half an hour to run.
Happily, in 2019 an upstream developer did the work to carefully
select a more appropriate set of tests to use for the profile:
https://github.com/python/cpython/commit/4e16a4a31https://bugs.python.org/issue36044
This suite takes just 2 minutes to run. And the resulting final
build is actually slightly faster than with the much longer suite,
at least as measured by those standard "pyperformance" benchmarks.
That work went into the 3.8 release, but the same list works great
if used on older releases too.
So, start passing that --enable-optimizations flag; and backport
that good-for-PGO set of tests, so that we use it on all releases.
This should enable (manual) building of RPMs from python projects using
the `python setup.py bdist_rpm` command on systems where `rpmbuild` is
not located in `/usr/bin/`. (e.g. NixOS)
The discovery of the rpmbuild command was fixed upstream in Python 3.8,
so this commit backports the relevant patch to our currently supported
Python 3 versions.
Fixes: #85204
The ./configure script prints a warning when passed this flag,
starting with 3.7:
configure: WARNING: unrecognized options: --with-threads
The reason is that there's no longer such a thing as a build
without threads.
Eliminate the warning, by only passing the flag on the older releases
that accept it.
Upstream change and discussion:
https://github.com/python/cpython/commit/a6a4dc816https://bugs.python.org/issue31370
The prefix will now be correct in case of Nix env.
Note, however, that creating a venv from a Nix env still does not function. This does not seem to be possible
with the current approach either, because venv will copy or symlink our Python wrapper. In case it symlinks
(the default) it won't see a pyvenv.cfg. If it is copied I think it should function but it does not...
This is needed in case of `python.buildEnv` to make sure site.PREFIXES
does not only point to the unwrapped executable prefix.
--------------------------------------------------------------------------------
This PR is a story where your valiant hero sets out on a very simple adventure but ends up having to slay dragons, starts questioning his own sanity and finally manages to gain enough knowledge to slay the evil dragon and finally win the proverbial price.
It all started out on sunny spring day with trying to tackle the Nixops plugin infrastructure and make that nice enough to work with.
Our story begins in the shanty town of [NixOps-AWS](https://github.com/nixos/nixops-aws) where [mypy](http://mypy-lang.org/) type checking has not yet been seen.
As our deuteragonist (@grahamc) has made great strides in the capital city of [NixOps](https://github.com/nixos/nixops) our hero wanted to bring this out into the land and let the people rejoice in reliability and a wonderful development experience.
The plugin work itself was straight forward and our hero quickly slayed the first small dragon, at this point things felt good and our hero thought he was going to reach the town of NixOps-AWS very quickly.
But alas! Mypy did not want to go, it said:
`Cannot find implementation or library stub for module named 'nixops'`
Our hero felt a small sliver of life escape from his body. Things were not going to be so easy.
After some frustration our hero discovered there was a [rule of the land of Python](https://www.python.org/dev/peps/pep-0561/) that governed the import of types into the kingdom, more specificaly a very special document (file) called `py.typed`.
Things were looking good.
But no, what the law said did not seem to match reality. How could things be so?
After some frustrating debugging our valiant hero thought to himself "Hmm, I wonder if this is simply a Nix idiosyncrasy", and it turns out indeed it was.
Things that were working in the blessed way of the land of Python (inside a `virtualenv`) were not working the way they were from his home town of Nix (`nix-shell` + `python.withPackages`).
After even more frustrating attempts at reading the mypy documentation and trying to understand how things were supposed to work our hero started questioning his sanity.
This is where things started to get truly interesting.
Our hero started to use a number of powerful weapons, both forged in the land of Python (pdb) & by the mages of UNIX (printf-style-debugging & strace).
After first trying to slay the dragon simply by `strace` and a keen eye our hero did not spot any weak points.
Time to break out a more powerful sword (`pdb`) which also did not divulge any secrets about what was wrong.
Our hero went back to the `strace` output and after a fair bit of thought and analysis a pattern started to emerge. Mypy was looking in the wrong place (i.e. not in in the environment created by `python.withPackages` but in the interpreter store path) and our princess was in another castle!
Our hero went to the pub full of old grumpy men giving out the inner workings of the open source universe (Github) and acquired a copy of Mypy.
He littered the code with print statements & break points.
After a fierce battle full of blood, sweat & tears he ended up in 20f7f2dd71/mypy/sitepkgs.py and realised that everything came down to the Python `site` module and more specifically https://docs.python.org/3.7/library/site.html#site.getsitepackages which in turn relies on https://docs.python.org/3.7/library/site.html#site.PREFIXES .
Our hero created a copy of the environment created by `python.withPackages` and manually modified it to confirm his findings, and it turned out it was indeed the case.
Our hero had damaged the dragon and it was time for a celebration.
He went out and acquired some mead which he ingested while he typed up his story and waited for the dragon to finally die (the commit caused a mass-rebuild, I had to wait for my repro).
In the end all was good in [NixOps-AWS](https://github.com/nixos/nixops-aws)-town and type checks could run. (PR for that incoming tomorrow).
- Replaced python override from the final stdenv, instead we
propagate our bootstrap python to stage4 and override both
CF and xnu to use it.
- Removed CF argument from python interpreters, this is redundant
since it's not overidden anymore.
- Inherit CF from stage4, making it the same as the stdenv.
When `makeWrapperArgs` variable is not set, `declare -p makeWrapperArgs`
will return with 1 and print an error message to stderr.
I did not handle the non-existence case in b0633406cb
because I thought `mk-python-derivation` will always define `makeWrapperArgs`
but `wrapProgram` can be called independently. And even with `mk-python-derivation`,
`makeWrappers` will not be set unless explicitly declared in the derivation
because of https://github.com/NixOS/nix/issues/1461.
I was lead to believe that because the builds were succeeding and I confirmed
that the mechanism fails when the variable is not defined and `-o nounset` is enabled.
It appears that `wrapPython` setup hook is not running under `-o nounset`, though,
invaldating the assumption.
Now we are checking that the variable exists before checking its type, which
will get rid of the warning and also prevent future error when `-o nounset`
is enabled in the setup hook.
For more information, see the discussion at
https://github.com/NixOS/nixpkgs/commit/a6bb2ede232940a96150da7207a3ecd15eb6328
Bash takes an assignment of a string to an array variable:
local -a user_args
user_args="(foo bar)"
to mean appending the string to the array, not parsing the string into
an array as is the case when on the same line as the declaration:
local -a user_args="(foo bar)"
b0633406cb extracted the declaration before
the newly branched code block, causing string makeWrapperArgs being added
to the array verbatim.
Since local is function scoped, it does not matter if we move it inside
each of the branches so we fix it this way.
When `makeWrapperArgs` is a Bash array, we only passed the first
item to `wrapProgram`. We need to use `"${makeWrapperArgs[@]}"`
to extract all the items. But that breaks the common string case so
we need to handle that case separately.
This will turn manylinux support back on by default.
PIP will now do runtime checks against the compatible glibc version to
determine if the current interpreter is compatible with a given
manylinux specification. However it will not check if any of the
required libraries are present.
The motivation here is that we want to support building python packages
with wheels that require manylinux support. There is no real change for
users of source builds as they are still buildings packages from source.
The real noticeable(?) change is that impure usages (e.g. running `pip
install package`) will install manylinux packages that previously
refused to install.
Previously we did claim that we were not compatible with manylinux and
thus they wouldn't be installed at all.
Now impure users will have basically the same situation as before: If
you require some wheel only package it didn't work before and will not
properly work now. Now the program will fail during runtime vs during
installation time.
I think it is a reasonable trade-off since it allows us to install
manylinux packages with nix expressions and enables tools like
poetry2nix.
This should be a net win for users as it allows wheels, that we
previously couldn't really support, to be used.
It's a year until the final release but this will give a chance to test
out certain features and how it integrates with other packages.
https://www.python.org/dev/peps/pep-0596/
There were no new changes in version 3.5.9; 3.5.9 was released only because of a CDN caching problem,
which resulted in some users downloading a prerelease version of the 3.5.8 .xz source tarball.
Apart from the version number, 3.5.9 is identical to the proper 3.5.8 release.
Go beyond the obvious setup hooks now, with a bit of sed, with a skipped case:
- cc-wrapper's `dontlink`, because it already is handled.
Also, in nix files escaping was manually added.
EMP
Python 3.8 fails to build on macOS for two reasons:
* python-3.x-distutils-C++.patch fails to apply cleanly.
* An #include for <util.h> is missing, causing a build failure:
./Modules/posixmodule.c:6586:9: error: implicit declaration of function 'openpty' is invalid in C99
if (openpty(&master_fd, &slave_fd, NULL, NULL, NULL) != 0)
^
Use the correct version of python-3.x-distutils-C++.patch, and add a
patch to #include <util.h>.
This commit splits the `buildPythonPackage` into multiple setup hooks.
Generally, Python packages are built from source to wheels using `setuptools`.
The wheels are then installed with `pip`. Tests were often called with
`python setup.py test` but this is less common nowadays. Most projects
now use a different entry point for running tests, typically `pytest`
or `nosetests`.
Since the wheel format was introduced more tools were built to generate these,
e.g. `flit`. Since PEP 517 is provisionally accepted, defining a build-system
independent format (`pyproject.toml`), `pip` can now use that format to
execute the correct build-system.
In the past I've added support for PEP 517 (`pyproject`) to the Python
builder, resulting in a now rather large builder. Furthermore, it was not possible
to reuse components elsewhere. Therefore, the builder is now split into multiple
setup hooks.
The `setuptoolsCheckHook` is included now by default but in time it should
be removed from `buildPythonPackage` to make it easier to use another hook
(curently one has to pass in `dontUseSetuptoolsCheck`).
We don’t want cpython picking up /Library/Frameworks and
/System/Library/Frameworks which contains Tcl.framework. Instead it
should use the one provided by Nix. this would not be an issue if
sandboxing was enabled, but unfortunately that has its own issues.
Fixes#66647
There ver very many conflicts, basically all due to
name -> pname+version. Fortunately, almost everything was auto-resolved
by kdiff3, and for now I just fixed up a couple evaluation problems,
as verified by the tarball job. There might be some fallback to these
conflicts, but I believe it should be minimal.
Hydra nixpkgs: ?compare=1538299
This builds Python without optional dependencies.
We can't just use python3.override, as things like
python3Minimal.withPackages would pass the wrong python derivation into
these modules.
Turns out fixing this only in importlib is not sufficient and we
need to backport CPython part of the fix too.
This patch is based on https://hg.python.org/cpython/rev/c16063765d3a
but because the code around is different there are some changes (C-strings
instead of Python objects etc.)
With this patch Tensorflow builds successfully on many-core machine.
This commit adds a Nix-specific module that recursively adds paths that
are on `NIX_PYTHONPATH` to `sys.path`. In order to process possible
`.pth` files `site.addsitedir` is used.
The paths listed in `PYTHONPATH` are added to `sys.path` afterwards, but
they will be added before the entries we add here and thus take
precedence.
The reason for adding support for this environment variable is that we
can set it in a wrapper without breaking support for `PYTHONPATH`.
This is python bug https://bugs.python.org/issue13146. Fixed since
python 3.4. It makes pyc creation atomic, preventing a race condition.
The patch has been rebased on our deterministic build patch.
It wasn't backported to python 2.7 because there was a complaint about
changed semantics. Since files are now created in a temporary directory
and then moved, symlinks will be overridden. See
https://bugs.python.org/issue17222.
That is an edge-case however. Ubuntu and debian have backported the fix
in 2013 already, making it mainstream enough for us to adopt.
Patching numpy.distutils used to be required for pythonPackages.cython
to build on darwin. It was later accidentally disabled during one of the
refactorings, but that did not break cython. This change reinstantiates
the patch. It still applies, so it should be low maintenance and it can
still be useful.
Originally introduced in 8970a9c and 1531b5e, these patches were lost in
efbe87f when the CPython version files were merged, likely due to
CPython 3.7 not needing them anymore. These patches should remain
in-tree until CPython 3.5 and 3.6 support is dropped completely.
Found with the diffoscope ( https://diffoscope.org/ ).
The upstream patch for distutils does not apply cleanly to Python
3.7.3's sources. (The patch applies cleanly to Python 3.7.2's sources,
but nixpkgs commit 0ddae82e6a upgraded
Python to 3.7.3.) Fix the patch to make python37 build on macOS.
The wrapper is not needed because the runpath is already set correctly,
and LD_LIBRARY_PATH was breaking child processes linked against
different libc versions.
Signed-off-by: Anders Kaseorg <andersk@mit.edu>
These interpreters are prebuilt by upstream and patched using patchelf.
They are primarily added for testing purposes and development on the
non-prebuilt PyPy interpreters as it can speed up translation
significantly.
Drop `python.majorVersion`. For Python language version, use `python.pythonVersion`.
For implementation version, use `python.sourceVersion`.
Some expressions were broken. Those that were identified were fixed.
fixup major
This changeset allows for cross-compilation of Python packages. Packages
built with buildPythonPackage are not allowed to refer to the build
machine. Executables that have shebangs will refer to the host.
Each time a new major/minor version of CPython was released, a new
expression would be written, typically copied from the previous release.
Often fixes are only made in the current/latest release. By merging the
expressions it's more likely that modifications end up in all versions,
as is likely intended.
This commit introduces one expression for Python 3, and another for 2.7.
These two may also be merged, but it will result in a lot of extra
conditionals making the expression harder to follow.
A common passthru is introduced for CPython and PyPy.
python 2.7: use common passthru
updateScript accepts a list, in which case, it will execute the head with the
tail as arguments. Switching to this style will allow us to get rid of the need
to create extra script doing just that.
