[PATCH] gnu: Add python-blis

Done

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3 participants

Ludovic Courtès
Artyom V. Poptsov
Vagrant Cascadian

Owner: unassigned

Submitted by: Artyom V. Poptsov

Severity: normal

Debbugs page

Artyom V. Poptsov wrote 3 years ago

Recipients:(address . guix-patches@gnu.org)

Message-ID:87tu9ifs3m.fsf@gmail.com

Hello,

this patch adds "blis" Python module[1] under the name "python-blis".

- Artyom

References:

1. "Fast matrix-multiplication as a self-contained Python library"

https://github.com/explosion/cython-blis

From 3d22d0e5f7929ac1b782217ec207a5e462316c66 Mon Sep 17 00:00:00 2001

* gnu/packages/python-xyz.scm (python-blis): New variable.

---

gnu/packages/python-xyz.scm | 24 ++++++++++++++++++++++++

1 file changed, 24 insertions(+)

Toggle diff (34 lines)diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 3c4fa16d16..95b85b9931 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -31449,3 +31449,27 @@ written in C.")
     (synopsis "Cython bindings for MurmurHash2")
     (description "This package provides Cython bindings for MurmurHash2.")
     (license license:expat)))
+
+(define-public python-blis
+  (package
+    (name "python-blis")
+    (version "0.9.0")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "blis" version))
+              (sha256
+               (base32
+                "0adl7knj11rglg6l9nfqccl8kgs2v1c7qllv9c5kf5k796hir7k9"))))
+    (build-system python-build-system)
+    (native-inputs (list python-pytest python-cython))
+    (inputs (list python python-numpy python-hypothesis))
+    (arguments
+     ;; XXX: Tests are failing with the following error:
+     ;; AttributeError: module 'numpy.__config__' has no attribute 'blas_ilp64_opt_info'
+     (list #:tests? #f))
+    (home-page "https://github.com/explosion/cython-blis")
+    (synopsis "Fast matrix-multiplication Python library")
+    (description
+     "This package provides the @url{https://github.com/flame/blis,
+Blis linear algebra} routines as a self-contained Python C-extension.")
+    (license license:bsd-3)))
-- 
2.25.1

-- 
Artyom "avp" Poptsov <poptsov.artyom@gmail.com>
Home page: https://memory-heap.org/~avp/
CADR Hackerspace co-founder: https://cadrspace.ru/
GPG: D0C2 EAC1 3310 822D 98DE  B57C E9C5 A2D9 0898 A02F

Ludovic Courtès wrote 3 years ago

Recipients:(name . Artyom V. Poptsov)(address . poptsov.artyom@gmail.com)(address . 55565@debbugs.gnu.org)

Message-ID:87pmjyd60l.fsf@gnu.org

Hi Artyom,

"Artyom V. Poptsov" <poptsov.artyom@gmail.com> skribis:

Toggle quote (7 lines)

> From 3d22d0e5f7929ac1b782217ec207a5e462316c66 Mon Sep 17 00:00:00 2001

> From: "Artyom V. Poptsov" <poptsov.artyom@gmail.com>

> Date: Sun, 22 May 2022 01:14:26 +0300

> Subject: [PATCH] gnu: Add python-blis

> * gnu/packages/python-xyz.scm (python-blis): New variable.

[...]

Toggle quote (7 lines)

> + (native-inputs (list python-pytest python-cython))

> + (inputs (list python python-numpy python-hypothesis))

> + (arguments

> + ;; XXX: Tests are failing with the following error:

> + ;; AttributeError: module 'numpy.__config__' has no attribute 'blas_ilp64_opt_info'

> + (list #:tests? #f))

Doesn’t that failure suggest something’s really wrong? Seems worth

investigating.

Toggle quote (6 lines)

> + (home-page "https://github.com/explosion/cython-blis")

> + (synopsis "Fast matrix-multiplication Python library")

> + (description

> + "This package provides the @url{https://github.com/flame/blis,

> +Blis linear algebra} routines as a self-contained Python C-extension.")

Blis isn’t listed in ‘inputs’, and apparently that’s because it’s

bundled.

Could you “unbundle” it? That is, add Blis as an input, make sure it

gets used during the build process, and remove the bundled copy.

Thanks in advance,

Ludo’.

Artyom V. Poptsov wrote 3 years ago

Recipients:(name . Ludovic Courtès)(address . ludo@gnu.org)(address . 55565@debbugs.gnu.org)

Message-ID:87pmjfxywd.fsf@gmail.com

Hello Ludovic,

thanks for the feedback.

I tried to fix the patch and got some promising results. Please find

the updated patch attached.

Basically I patched 'blis/benchmark.py' to use "blas_opt_info" instead

of "blas_ilp64_opt_info" and tests went fine. An issue with different

numpy versions I guess? I also added "blis" and "python-numpy-next" to

the "native-inputs".

- Artyom

From 3d088c0cbeee76c59dc140db16119a5e3f837b08 Mon Sep 17 00:00:00 2001

* gnu/packages/python-xyz.scm (python-blis): New variable.

---

gnu/packages/python-xyz.scm | 36 ++++++++++++++++++++++++++++++++++++

1 file changed, 36 insertions(+)

Toggle diff (46 lines)diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 5f9ce4fdfe..934dfd2959 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -29435,3 +29435,39 @@ Information about these scales can be
 @url{https://en.wikipedia.org/wiki/List_of_musical_scales_and_modes, found on
 Wikipedia}.")
     (license license:expat)))
+
+(define-public python-blis
+  (package
+    (name "python-blis")
+    (version "0.9.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/explosion/cython-blis")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "1p4y4mf8046kv2syf2s0v6mf4s000anr1ws7w3fny852gpp6czk4"))))
+    (build-system python-build-system)
+    (native-inputs (list python-numpy-next
+                         python-pytest
+                         python-cython
+                         blis
+                         python-hypothesis))
+    (arguments
+     (list #:tests? #t
+           #:phases
+           #~(modify-phases %standard-phases
+               (add-after 'unpack 'patch
+                 (lambda _
+                   (substitute* "./blis/benchmark.py"
+                     (("blas_ilp64_opt_info")
+                      "blas_opt_info")))))))
+    (home-page "https://github.com/explosion/cython-blis")
+    (synopsis "Fast matrix-multiplication Python library")
+    (description
+     "This package provides the @url{https://github.com/flame/blis,
+Blis linear algebra} routines as a self-contained Python C-extension.")
+    (license license:bsd-3)))
-- 
2.25.1

-- 
Artyom "avp" Poptsov <poptsov.artyom@gmail.com>
Home page: https://memory-heap.org/~avp/
CADR Hackerspace co-founder: https://cadrspace.ru/
GPG: D0C2 EAC1 3310 822D 98DE  B57C E9C5 A2D9 0898 A02F

Ludovic Courtès wrote 3 years ago

Recipients:(name . Artyom V. Poptsov)(address . poptsov.artyom@gmail.com)(address . 55565@debbugs.gnu.org)

Message-ID:87wndksw4d.fsf@gnu.org

Hi Artyom,

"Artyom V. Poptsov" <poptsov.artyom@gmail.com> skribis:

Toggle quote (5 lines)

> Basically I patched 'blis/benchmark.py' to use "blas_opt_info" instead

> of "blas_ilp64_opt_info" and tests went fine. An issue with different

> numpy versions I guess? I also added "blis" and "python-numpy-next" to

> the "native-inputs".

Unfortunately this is not sufficient: the source bundles a copy of BLIS

under ‘blis/_src’ and it starts by building it (which is why it takes so

long), whether or not BLIS is among the inputs.

Could you (1) add a snippet that removes ‘blis/_src’, and (2) see

whether/how ‘setup.py’ can be patched to not build BLIS? It might be

that commenting out the line that reads:

cmdclass={"build_ext": ExtensionBuilder},

would be enough, I don’t know.

Anyhow, given that BLIS is the kind of package that’s highly tuned on

our side for performance and reproducibility configuration, it’s

important to not have several copies around.

Toggle quote (6 lines)

> + (native-inputs (list python-numpy-next

> + python-pytest

> + python-cython

> + blis

> + python-hypothesis))

NumPy and BLIS should definitely be ‘inputs’, not ‘native-inputs’; not

sure about ‘hypothesis’.

Also, please include a short comment explaining why numpy-next is used

rather than numpy (like “version >= X.Y required”).

Could you send an updated patch?

Sorry that this is providing trickier than we’d like!

Thanks,

Ludo’.

Vagrant Cascadian wrote 2 years ago

Re: [bug#55565] [PATCH] gnu: Add python-blis

Recipients:

Message-ID:87a5u5qw9c.fsf@wireframe

On 2022-05-22, Artyom V. Poptsov wrote:

Toggle quote (3 lines)

> Subject: [PATCH] gnu: Add python-blis

> * gnu/packages/python-xyz.scm (python-blis): New variable.

...

Toggle quote (5 lines)

> +(define-public python-blis

> + (package

> + (name "python-blis")

> + (version "0.9.0")

python-blis 0.9.1 was added in:

069618522d3ee040e0b0f2d9f24ceb763ce434aa gnu: Add python-blis.

Marking as done.

live well,

vagrant

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