* [PATCH] Replace ATLAS with OpenBLAS (+lapack)
@ 2015-06-12 9:41 Ricardo Wurmus
2015-06-14 22:04 ` Ludovic Courtès
0 siblings, 1 reply; 3+ messages in thread
From: Ricardo Wurmus @ 2015-06-12 9:41 UTC (permalink / raw)
To: Guix-devel
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Hi Guix,
attached are three more patches to replace ATLAS with OpenBLAS in
python.scm.
I noticed that numpy also needs "lapack", because OpenBLAS is built with
"NO_LAPACK=1". That's what the first patch is for.
This is also important for the second patch which makes python-scipy use
OpenBLAS and Lapack instead of ATLAS.
The final patch replaces "atlas" with "openblas" in the
python-scikit-learn package definition.
~~ Ricardo
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[-- Attachment #2: 0001-gnu-python-numpy-bootstrap-Add-lapack-to-inputs.patch --]
[-- Type: text/x-patch, Size: 1891 bytes --]
From aeb4f541486d5bb02d4002380e8f7be49967b10d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Fri, 12 Jun 2015 10:48:58 +0200
Subject: [PATCH 1/3] gnu: python-numpy-bootstrap: Add lapack to inputs.
* gnu/packages/python.scm (python-numpy-bootstrap)[inputs]: Add lapack to
inputs, because OpenBLAS does not include lapack functions.
---
gnu/packages/python.scm | 17 ++++++++++++++---
1 file changed, 14 insertions(+), 3 deletions(-)
diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 914c2dc..d753cd3 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -2283,7 +2283,8 @@ writing C extensions for Python as easy as Python itself.")
(build-system python-build-system)
(inputs
`(("python-nose" ,python-nose)
- ("openblas" ,openblas)))
+ ("openblas" ,openblas)
+ ("lapack" ,lapack)))
(native-inputs
`(("gfortran" ,gfortran-4.8)))
(arguments
@@ -2293,11 +2294,21 @@ writing C extensions for Python as easy as Python itself.")
(lambda* (#:key inputs #:allow-other-keys)
(call-with-output-file "site.cfg"
(lambda (port)
- (format port "[openblas]
+ (format port
+ "[openblas]
libraries = openblas
library_dirs = ~a/lib
include_dirs = ~a/include
-" (assoc-ref inputs "openblas") (assoc-ref inputs "openblas"))))
+
+[lapack]
+lapack_libs = lapack
+library_dirs = ~a/lib
+include_dirs = ~a/include
+"
+ (assoc-ref inputs "openblas")
+ (assoc-ref inputs "openblas")
+ (assoc-ref inputs "lapack")
+ (assoc-ref inputs "lapack"))))
;; Use "gcc" executable, not "cc".
(substitute* "numpy/distutils/system_info.py"
(("c = distutils\\.ccompiler\\.new_compiler\\(\\)")
--
2.1.0
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[-- Attachment #3: 0002-gnu-python-scipy-Build-with-OpenBLAS-and-lapack.patch --]
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From a26127d8ecd9170d11350f7085c9e39aa4018b4a Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Fri, 12 Jun 2015 11:30:51 +0200
Subject: [PATCH 2/3] gnu: python-scipy: Build with OpenBLAS and lapack.
* gnu/packages/python.scm (python-scipy)[inputs]: Remove "atlas", add "lapack"
and "openblas".
* gnu/packages/python.scm (python-scipy)[arguments]: Replace phase
"set-environment-variables" with "configure-openblas".
---
gnu/packages/python.scm | 30 ++++++++++++++++++------------
1 file changed, 18 insertions(+), 12 deletions(-)
diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index d753cd3..832bb2d 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -2628,7 +2628,8 @@ toolkits.")
("python-pyparsing" ,python-pyparsing)
("python-nose" ,python-nose)
("python-sphinx" ,python-sphinx)
- ("atlas" ,atlas)))
+ ("lapack" ,lapack)
+ ("openblas" ,openblas)))
(native-inputs
`(("gfortran" ,gfortran-4.8)
("texlive" ,texlive)
@@ -2637,18 +2638,23 @@ toolkits.")
(arguments
`(#:phases
(alist-cons-before
- 'build 'set-environment-variables
+ 'build 'configure-openblas
(lambda* (#:key inputs #:allow-other-keys)
- (let* ((atlas-threaded
- (string-append (assoc-ref inputs "atlas")
- "/lib/libtatlas.so"))
- ;; On single core CPUs only the serial library is created.
- (atlas-lib
- (if (file-exists? atlas-threaded)
- atlas-threaded
- (string-append (assoc-ref inputs "atlas")
- "/lib/libsatlas.so"))))
- (setenv "ATLAS" atlas-lib)))
+ (call-with-output-file "site.cfg"
+ (lambda (port)
+ (format port
+ "[blas]
+libraries = openblas
+library_dirs = ~a/lib
+include_dirs = ~a/include
+[atlas]
+library_dirs = ~a/lib
+atlas_libs = openblas
+"
+ (assoc-ref inputs "openblas")
+ (assoc-ref inputs "openblas")
+ (assoc-ref inputs "openblas"))))
+ #t)
(alist-cons-after
'install 'install-doc
(lambda* (#:key outputs #:allow-other-keys)
--
2.1.0
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[-- Attachment #4: 0003-gnu-python-scikit-learn-Use-OpenBLAS-instead-of-ATLA.patch --]
[-- Type: text/x-patch, Size: 2863 bytes --]
From 79d29126037cd227b01b3a193bf016ec9e12b4fb Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Fri, 12 Jun 2015 11:34:39 +0200
Subject: [PATCH 3/3] gnu: python-scikit-learn: Use OpenBLAS instead of ATLAS.
* gnu/packages/python.scm (python-scikit-learn)[inputs]: Replace "atlas" with
"openblas".
---
gnu/packages/python.scm | 43 +++++++++++++++----------------------------
1 file changed, 15 insertions(+), 28 deletions(-)
diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 832bb2d..5f9d487 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -2080,35 +2080,22 @@ sources.")
(arguments
`(#:phases
(alist-cons-before
- 'build 'set-environment-variables
- (lambda* (#:key inputs #:allow-other-keys)
- (let* ((atlas-threaded
- (string-append (assoc-ref inputs "atlas")
- "/lib/libtatlas.so"))
- ;; On single core CPUs only the serial library is created.
- (atlas-lib
- (if (file-exists? atlas-threaded)
- atlas-threaded
- (string-append (assoc-ref inputs "atlas")
- "/lib/libsatlas.so"))))
- (setenv "ATLAS" atlas-lib)))
- (alist-cons-before
- 'check 'set-HOME
- ;; some tests require access to "$HOME"
- (lambda _ (setenv "HOME" "/tmp"))
- ;; Tests can only be run after the library has been installed and not
- ;; within the source directory.
- (alist-cons-after
- 'install 'check
- (lambda _
- (with-directory-excursion "/tmp"
- ;; With Python 3 one test of 3334 fails
- ;; (sklearn.tests.test_common.test_transformers); see
- ;; https://github.com/scikit-learn/scikit-learn/issues/3693
- (system* "nosetests" "-v" "sklearn")))
- (alist-delete 'check %standard-phases))))))
+ 'check 'set-HOME
+ ;; some tests require access to "$HOME"
+ (lambda _ (setenv "HOME" "/tmp"))
+ ;; Tests can only be run after the library has been installed and not
+ ;; within the source directory.
+ (alist-cons-after
+ 'install 'check
+ (lambda _
+ (with-directory-excursion "/tmp"
+ ;; With Python 3 one test of 3334 fails
+ ;; (sklearn.tests.test_common.test_transformers); see
+ ;; https://github.com/scikit-learn/scikit-learn/issues/3693
+ (system* "nosetests" "-v" "sklearn")))
+ (alist-delete 'check %standard-phases)))))
(inputs
- `(("atlas" ,atlas)
+ `(("openblas" ,openblas)
("python-nose" ,python-nose)))
(propagated-inputs
`(("python-numpy" ,python-numpy)
--
2.1.0
^ permalink raw reply related [flat|nested] 3+ messages in thread
* Re: [PATCH] Replace ATLAS with OpenBLAS (+lapack)
2015-06-12 9:41 [PATCH] Replace ATLAS with OpenBLAS (+lapack) Ricardo Wurmus
@ 2015-06-14 22:04 ` Ludovic Courtès
2015-06-15 8:44 ` Ricardo Wurmus
0 siblings, 1 reply; 3+ messages in thread
From: Ludovic Courtès @ 2015-06-14 22:04 UTC (permalink / raw)
To: Ricardo Wurmus; +Cc: Guix-devel
Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> skribis:
> attached are three more patches to replace ATLAS with OpenBLAS in
> python.scm.
Good!
> From aeb4f541486d5bb02d4002380e8f7be49967b10d Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Fri, 12 Jun 2015 10:48:58 +0200
> Subject: [PATCH 1/3] gnu: python-numpy-bootstrap: Add lapack to inputs.
>
> * gnu/packages/python.scm (python-numpy-bootstrap)[inputs]: Add lapack to
> inputs, because OpenBLAS does not include lapack functions.
OK.
> From a26127d8ecd9170d11350f7085c9e39aa4018b4a Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Fri, 12 Jun 2015 11:30:51 +0200
> Subject: [PATCH 2/3] gnu: python-scipy: Build with OpenBLAS and lapack.
>
> * gnu/packages/python.scm (python-scipy)[inputs]: Remove "atlas", add "lapack"
> and "openblas".
> * gnu/packages/python.scm (python-scipy)[arguments]: Replace phase
> "set-environment-variables" with "configure-openblas".
OK.
> From 79d29126037cd227b01b3a193bf016ec9e12b4fb Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Fri, 12 Jun 2015 11:34:39 +0200
> Subject: [PATCH 3/3] gnu: python-scikit-learn: Use OpenBLAS instead of ATLAS.
>
> * gnu/packages/python.scm (python-scikit-learn)[inputs]: Replace "atlas" with
> "openblas".
Please mention how the phases are modified in the commit log.
Otherwise OK.
Thanks!
Ludo’.
^ permalink raw reply [flat|nested] 3+ messages in thread
* Re: [PATCH] Replace ATLAS with OpenBLAS (+lapack)
2015-06-14 22:04 ` Ludovic Courtès
@ 2015-06-15 8:44 ` Ricardo Wurmus
0 siblings, 0 replies; 3+ messages in thread
From: Ricardo Wurmus @ 2015-06-15 8:44 UTC (permalink / raw)
To: Ludovic Courtès; +Cc: Guix-devel
Ludovic Courtès <ludo@gnu.org> writes:
> Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> skribis:
>
>> attached are three more patches to replace ATLAS with OpenBLAS in
>> python.scm.
[...]
>> From 79d29126037cd227b01b3a193bf016ec9e12b4fb Mon Sep 17 00:00:00 2001
>> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
>> Date: Fri, 12 Jun 2015 11:34:39 +0200
>> Subject: [PATCH 3/3] gnu: python-scikit-learn: Use OpenBLAS instead of ATLAS.
>>
>> * gnu/packages/python.scm (python-scikit-learn)[inputs]: Replace "atlas" with
>> "openblas".
>
> Please mention how the phases are modified in the commit log.
I updated the commit log and pushed the three commits. Thank you for
the review!
~~ Ricardo
^ permalink raw reply [flat|nested] 3+ messages in thread
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