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Re: [Distutils] PEP for dependencies on libraries like BLAS (was: Re: Working toward Linux wheel support)

From: David Cournapeau <cour...@gmail.com>
Fri, 14 Aug 2015 10:59:02 +0100
On Thu, Aug 13, 2015 at 7:08 AM, Nathaniel Smith <n...@pobox.com> wrote:

> On Wed, Aug 12, 2015 at 8:10 PM, Robert Collins> <robe...@robertcollins.net> wrote:> > On 13 August 2015 at 12:51, Nathaniel Smith <n...@pobox.com> wrote:> >> On Aug 12, 2015 16:49, "Robert Collins" <robe...@robertcollins.net>> wrote:> >>>> >>> I'm not sure what will be needed to get the PR accepted; At PyCon AU> >>> Tennessee Leuwenberg started drafting a PEP for the expression of> >>> dependencies on e.g. BLAS - its been given number 497, and is in the> >>> packaging-peps repo; I'm working on updating it now.> >>> >> I wanted to take a look at this PEP, but I can't seem to find it. PEP> 497:> >>   https://www.python.org/dev/peps/pep-0497/> >> appears to be something else entirely?> >>> >> I'm a bit surprised to hear that such a PEP is needed. We (= numpy devs)> >> have actively been making plans to ship a BLAS wheel on windows, and> AFAICT> >> this is totally doable now -- the blocker is windows toolchain issues,> not> >> pypa-related infrastructure.> >>> >> Specifically the idea is to have a wheel that contains the shared> library as> >> a regular old data file, plus a stub python package that knows how to> find> >> this data file and how to make it accessible to the linker. So> >> numpy/__init__.py would start by calling:> >>> >> import pyopenblas1> >> # on Linux modifies LD_LIBRARY_PATH,> >> # on Windows uses ctypes to preload... whatever> >> pyopenblas1.enable()> >>> >> and then get on with things, or the build system might do:> >>> >> import pyopenblas1> >> pyopenblas1.get_header_directories()> >> pyopenblas1.get_linker_directories()> >>>> Thanks to James for sending on the link!>> Two main thoughts, now that I've read it over:>> 1) The motivating example is somewhat confused -- the draft says:>> + The example provided in the abstract is a> + hypothetical package which needs versions of numpy and scipy, both of> which> + must have been compiled to be aware of the ATLAS compiled set of> linear algebra> + libraries (for performance reasons). This sounds esoteric but is, in> fact, a> + routinely encountered situation which drives people towards using the> + alternative packaging for scientific python environments.>> Numpy and scipy actually work hard to export a consistent, append-only> ABI regardless of what libraries are used underneath. (This is> actually by far our biggest issue with wheels -- that there's still no> way to tag the numpy ABI as part of the ABI string, so in practice> it's just impossible to ever have a smooth migration to a new ABI and> we have no choice but to forever maintain compatibility with numpy> 0.1. But that's not what this proposal addresses.) Possibly part of> the confusion here is that Christoph Gohlke's popular numpy+scipy> builds use a hack where instead of making the wheels self-contained> via statically linking or something like that, then he ships the> actual libBLAS.dll inside the numpy wheel, and then the scipy wheel> has some code added that magically "knows" that there is this special> numpy wheel that it can find libBLAS.dll inside and use it directly> from scipy's own extensions. But this coupling is pretty much just> broken, and it directly motivates the blas-in-its-own-wheel design I> sketched out above.>> (I guess the one exception is that if you have a numpy or scipy build> that dynamically links to a library like BLAS, and then another> extension that links to a different BLAS with an incompatible ABI, and> the two BLAS libraries have symbol name collisions, then that could be> a problem because ELF is frustrating like that. But the obvious> solution here is to be careful about how you do your builds -- either> by using static linking, or making sure that incompatible ABIs get> different symbol names.)>> Anyway, this doesn't particularly undermine the PEP, but it would be> good to use a more realistic motivating example.>> 2) AFAICT, the basic goal of this PEP is to provide machinery to let> one reliably build a wheel for some specific version of some specific> distribution, while depending on vendor-provided libraries for various> external dependencies, and providing a nice user experience (e.g.,> telling users explicitly which vendor-provided libraries they need to> install). I say this because strings like "libblas1.so" or "kernel.h"> do not define any fixed ABI or APIs, unless you are implicitly scoping> to some particular distribution with at least some minimum version> constraint.>> It seems like a reasonable effort at solving this problem, and I guess> there are probably some people somewhere that have this problem, but> my concern is that I don't actually know any of those people. The> developers I know instead have the problem of, they want to be able to> provide a small finite number of binaries (ideally six binaries per> Python version: {32 bit, 64 bit} * {windows, osx, linux}) that> together will Just Work on 99% of end-user systems. And that's the> problem that Enthought, Continuum, etc., have been solving for years,> and which wheels already mostly solve on windows and osx, so it seems> like a reasonable goal to aim for. But I don't see how this PEP gets> us any closer to that. Again, not really a criticism -- these goals> aren't contradictory and it's great if pip ends up being able to> handle both common and niche use cases. But I want to make sure that> we're clear that these goals are different and which one each proposal> is aimed at.>> >> This doesn't help if you want to declare dependencies on external,> system> >> managed libraries and have those be automatically somehow provided or> >> checked for, but to me that sounds like an impossible boil-the-ocean> project> >> anyway, while the above is trivial and should just work.> >> > Well, have a read of the draft.> >> > Its a solved problem by e.g. conda, apt, yum, nix and many others.>> None of these projects allow a .deb to depend on .rpms etc. -- they> all require that they own the whole world with some narrow, carefully> controlled exceptions (e.g. anaconda requires some non-trivial runtime> on the host system -- glibc, glib, pcre, expat, ... -- but it's a> single fixed set that they've empirically determined is close enough> to universally available in practice). The "boil the ocean" part is> the part where everybody who wants to distribute wheels has to go> around and figure out every possible permutation of ABIs on every> possible external packaging system and provide separate wheels for> each of them.>> > Uploading system .so's is certainly also an option, and I see no> > reason why we can't do both.> >> > I do know that distribution vendors are likely to be highly allergic> > to the idea of having regular shared libraries present as binaries,> > but thats a different discussion :)>> Yeah, but basically in the same way that they're allergic to all> wheels, period, so ... :-). I think in the long run the only realistic> approach is for most users to either be getting blas+numpy from some> external system like macports/conda/yum/... or else to be getting> blas+numpy from official wheels on pypi. And neither of these two> scenarios seems to benefit from the functionality described in this> PEP.>> (Final emphasis: this is all just my own opinion based on my> far-from-omniscient view of the packaging system, please tell me if> I'm making some ridiculous error, or if well-actually libBLAS is> special and there is some other harder case I'm not thinking of, etc.)>

From my own experience if you have a design that covers blas/lapack issues
for numpy/scipy, you've solved a majority of typical binary packaging
issues in the python ecosystem.

Will you be there at euroscipy ? I will spend some time at Euroscipy to
continue the work we started at pycon around some of this (taking into
account the PEP as well).


> -n>> --> Nathaniel J. Smith -- http://vorpus.org> _______________________________________________> Distutils-SIG maillist  -  Dist...@python.org> https://mail.python.org/mailman/listinfo/distutils-sig>

Distutils-SIG maillist  -  Dist...@python.org

Recent Messages in this Thread
Nathaniel Smith Aug 13, 2015 12:51 am
James Polley Aug 13, 2015 01:02 am
Olivier Grisel Aug 13, 2015 03:06 am
Robert Collins Aug 13, 2015 03:10 am
Nathaniel Smith Aug 13, 2015 06:08 am
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