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[alpine-devel] [PATCH 1/2] Add testing/openblas.

Isaac Dunham <ibid.ag@gmail.com>
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<1409264344-5879-1-git-send-email-ibid.ag@gmail.com>
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Patch: +87 -0
OpenBLAS is a fast implementation of BLAS that's easier to build than ATLAS;
it also includes LAPACK support.
---
 testing/openblas/00-cpuid.patch | 34 ++++++++++++++++++++++++++
 testing/openblas/APKBUILD       | 53 +++++++++++++++++++++++++++++++++++++++++
 2 files changed, 87 insertions(+)
 create mode 100644 testing/openblas/00-cpuid.patch
 create mode 100644 testing/openblas/APKBUILD

diff --git a/testing/openblas/00-cpuid.patch b/testing/openblas/00-cpuid.patch
new file mode 100644
index 0000000..7758b46
--- /dev/null
+++ b/testing/openblas/00-cpuid.patch
@@ -0,0 +1,34 @@
commit db7e6366cd86b57cd0712293968938058288bde0
Author: Isaac Dunham <ibid.ag@gmail.com>
Date:   Thu Aug 28 13:05:07 2014 -0700

    Workaround PIC limitations in cpuid.
    
    cpuid uses register ebx, but ebx is reserved in PIC.
    So save ebx, swap ebx & edi, and return edi.
    
    Copied from Igor Pavlov's equivalent fix for 7zip (in CpuArch.c),
    which is public domain and thus OK license-wise.

diff --git a/cpuid_x86.c b/cpuid_x86.c
index 53016e1..f9df722 100644
--- a/cpuid_x86.c
+++ b/cpuid_x86.c
@@ -59,9 +59,16 @@
 void cpuid(int op, int *eax, int *ebx, int *ecx, int *edx);
 #else
 static inline void cpuid(int op, int *eax, int *ebx, int *ecx, int *edx){
+#if defined(__i386__) && defined(__PIC__)
+  __asm__ __volatile__
+    ("mov %%ebx, %%edi;"
+     "cpuid;"
+     "xchgl %%ebx, %%edi;"
+     : "=a" (*eax), "=D" (*ebx), "=c" (*ecx), "=d" (*edx) : "a" (op) : "cc");
+#else
   __asm__ __volatile__
     ("cpuid": "=a" (*eax), "=b" (*ebx), "=c" (*ecx), "=d" (*edx) : "a" (op) : "cc");
-
+#endif
 }
 #endif
 
diff --git a/testing/openblas/APKBUILD b/testing/openblas/APKBUILD
new file mode 100644
index 0000000..ce6f2fc
--- /dev/null
+++ b/testing/openblas/APKBUILD
@@ -0,0 +1,53 @@
# Contributor: Isaac Dunham <ibid.ag@gmail.com>
# Maintainer: Isaac Dunham <ibid.ag@gmail.com>
pkgname=openblas
pkgver=0.2.11
pkgrel=0
pkgdesc="A fast BSD-licensed BLAS based on gotoBLAS2, with LAPACK"
url="http://www.openblas.net"
arch="all"
license="BSD"
depends=""
depends_dev="gfortran"
makedepends="$depends_dev"
install=""
subpackages="$pkgname-dev $pkgname-doc"
source="$pkgname-$pkgver.tar.gz::http://github.com/xianyi/OpenBLAS/archive/v$pkgver.tar.gz
	00-cpuid.patch"

_builddir="$srcdir"/OpenBLAS-$pkgver
prepare() {
	local i
	cd "$_builddir"
	for i in $source; do
		case $i in
		*.patch) msg $i; patch -p1 -i "$srcdir"/$i || return 1;;
		esac
	done
}

build() {
	cd "$_builddir"
#USE_OPENMP=0: see GCC bug 60035
#NO_AFFINITY: don't expect to work on musl, also breaks R
#DYNAMIC_ARCH=1 requires 00-cpuid.patch
	make USE_OPENMP=0 NO_LAPACK=0 NUM_THREADS=8 MAJOR_VERSION=3 \
	NO_AFFINITY=1 DYNAMIC_ARCH=1 PREFIX=/usr || return 1
}

package() {
	cd "$_builddir"
	mkdir -pm 0755 "$pkgdir/usr/lib" "$pkgdir/usr/include" \
	"$pkgdir/usr/share/doc/$pkgname" || return 1
	make USE_OPENMP=0 NO_LAPACK=0 NUM_THREADS=2 MAJOR_VERSION=3 \
	NO_AFFINITY=1 DYNAMIC_ARCH=1 PREFIX="$pkgdir/usr" install || return 1
	for FILE in *.txt *.md LICENSE; do
		install -m 0644 $FILE "$pkgdir/usr/share/doc/$pkgname" || return 1
	done
}
md5sums="c456f3c5e84c3ab69ef89b22e616627a  openblas-0.2.11.tar.gz
0b8b59052a6387fe4aa9e3e473b3749b  00-cpuid.patch"
sha256sums="dc06836e700ef26519933af309a25958150693c376a536fe35d633d76f1a5606  openblas-0.2.11.tar.gz
65a809e9f0f06fd9ccefd0af6bc7c398fefe011404f699926946320783050d8b  00-cpuid.patch"
sha512sums="68abdf8366d4766fe5d852ca3850ea6236d4dc5bad044fa4116ca60872716003746bcfdb1005aac87533d9a085ae319ef18b7ed6f293baf88c79fd7c8562c9f0  openblas-0.2.11.tar.gz
1f41a324a9f233ef5fe037cd16c4aeabaf5895ba42e2f3758f8bb7a2cddda967fc01df50d86218f316d9406bb6ced4e91d4aec8119fc8f9c2f11b4ecf24e551f  00-cpuid.patch"
-- 
2.1.0



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[alpine-devel] [PATCH 2/2] testing/py-numpy: upgrade, use OpenBLAS

Isaac Dunham <ibid.ag@gmail.com>
Details
Message ID
<1409264344-5879-2-git-send-email-ibid.ag@gmail.com>
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<1409264344-5879-1-git-send-email-ibid.ag@gmail.com> (view parent)
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Patch: +168 -6
Upgraded to 1.8.1 so I could build with OpenBLAS.
Fixed a typo while I was here.
---
 testing/py-numpy/APKBUILD |  17 +++--
 testing/py-numpy/site.cfg | 157 ++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 168 insertions(+), 6 deletions(-)
 create mode 100644 testing/py-numpy/site.cfg

diff --git a/testing/py-numpy/APKBUILD b/testing/py-numpy/APKBUILD
index a590ba1..db7f1f8 100644
--- a/testing/py-numpy/APKBUILD
+++ b/testing/py-numpy/APKBUILD
@@ -2,7 +2,7 @@
# Maintainer: Francesco Colista <francesco.colista@gmail.com>
pkgname=py-numpy
_pkgname=numpy
pkgver=1.7.1
pkgver=1.8.1
pkgrel=0
pkgdesc="Scientific tools for Python"
url="http://numpy.scipy.org/"
@@ -13,7 +13,8 @@ depends_dev="python-dev"
makedepends="$depends_dev"
install=""
subpackages="$pkgname-dev $pkgname-doc"
source="http://downloads.sourceforge.net/$_pkgname/$_pkgname-$pkgver.tar.gz"
source="http://downloads.sourceforge.net/$_pkgname/$_pkgname-$pkgver.tar.gz
	site.cfg"

_builddir="$srcdir"/$_pkgname-$pkgver
prepare() {
@@ -22,13 +23,14 @@ prepare() {
	for i in $source; do
		case $i in
		*.patch) msg $i; patch -p1 -i "$srcdir"/$i || return 1;;
		site.cfg) msg $i; cp "$srcdir"/$i ./ || return 1;;
		esac
	done
}

build() {
	cd "$_builddir"
	export Atles=None
	export Atlas=None
	LDFLAGS="$LDFLAGS -shared"
	python setup.py build config_fc --fcompiler=gnu95  || return 1
}
@@ -41,6 +43,9 @@ package() {
	install -m644 LICENSE.txt "$pkgdir"/usr/share/licenses/custom/$pkgname/LICENSE
}

md5sums="0ab72b3b83528a7ae79c6df9042d61c6  numpy-1.7.1.tar.gz"
sha256sums="5525019a3085c3d860e6cfe4c0a30fb65d567626aafc50cf1252a641a418084a  numpy-1.7.1.tar.gz"
sha512sums="d58177f3971b6d07baf6f81a2088ba371c7e43ea64ee7ada261da97c6d725b4bd4927122ac373c55383254e4e31691939276dab08a79a238bfa55172a3eff684  numpy-1.7.1.tar.gz"
md5sums="be95babe263bfa3428363d6db5b64678  numpy-1.8.1.tar.gz
6f15bb8fe3d12faa8983a9e18bbea2a9  site.cfg"
sha256sums="3d722fc3ac922a34c50183683e828052cd9bb7e9134a95098441297d7ea1c7a9  numpy-1.8.1.tar.gz
8aa71c1aec2a9fdf6ab6167c92e86bdaf27f9a263b6b9849097ec7dcdf6d91a3  site.cfg"
sha512sums="39ef9e13f8681a2c2ba3d74ab96fd28c5669e653308fd1549f262921814fa7c276ce6d9fb65ef135006584c608bdf3db198d43f66c9286fc7b3c79803dbc1f57  numpy-1.8.1.tar.gz
21ca8db304cbbf5949f07702f2a42bb5e5a0d641921e36649555a41b0e48f04e96f53760417823177ac27f6de24b2191e6e1d5f0eb393beafa29f7484e23284f  site.cfg"
diff --git a/testing/py-numpy/site.cfg b/testing/py-numpy/site.cfg
new file mode 100644
index 0000000..effb46f
--- /dev/null
+++ b/testing/py-numpy/site.cfg
@@ -0,0 +1,157 @@
# This file provides configuration information about non-Python dependencies for
# numpy.distutils-using packages. Create a file like this called "site.cfg" next
# to your package's setup.py file and fill in the appropriate sections. Not all
# packages will use all sections so you should leave out sections that your
# package does not use.

# To assist automatic installation like easy_install, the user's home directory
# will also be checked for the file ~/.numpy-site.cfg .

# The format of the file is that of the standard library's ConfigParser module.
#
#   http://www.python.org/doc/current/lib/module-ConfigParser.html
#
# Each section defines settings that apply to one particular dependency. Some of
# the settings are general and apply to nearly any section and are defined here.
# Settings specific to a particular section will be defined near their section.
#
#   libraries
#       Comma-separated list of library names to add to compile the extension
#       with. Note that these should be just the names, not the filenames. For
#       example, the file "libfoo.so" would become simply "foo".
#           libraries = lapack,f77blas,cblas,atlas
#
#   library_dirs
#       List of directories to add to the library search path when compiling
#       extensions with this dependency. Use the character given by os.pathsep
#       to separate the items in the list. Note that this character is known to
#       vary on some unix-like systems; if a colon does not work, try a comma.
#       This also applies to include_dirs and src_dirs (see below).
#       On UN*X-type systems (OS X, most BSD and Linux systems):
#           library_dirs = /usr/lib:/usr/local/lib
#       On Windows:
#           library_dirs = c:\mingw\lib,c:\atlas\lib
#       On some BSD and Linux systems:
#           library_dirs = /usr/lib,/usr/local/lib
#
#   include_dirs
#       List of directories to add to the header file earch path.
#           include_dirs = /usr/include:/usr/local/include
#
#   src_dirs 
#       List of directories that contain extracted source code for the
#       dependency. For some dependencies, numpy.distutils will be able to build
#       them from source if binaries cannot be found. The FORTRAN BLAS and
#       LAPACK libraries are one example. However, most dependencies are more
#       complicated and require actual installation that you need to do
#       yourself.
#           src_dirs = /home/rkern/src/BLAS_SRC:/home/rkern/src/LAPACK_SRC
#
#   search_static_first
#       Boolean (one of (0, false, no, off) for False or (1, true, yes, on) for
#       True) to tell numpy.distutils to prefer static libraries (.a) over
#       shared libraries (.so). It is turned off by default.
#           search_static_first = false

# Defaults
# ========
# The settings given here will apply to all other sections if not overridden.
# This is a good place to add general library and include directories like
# /usr/local/{lib,include}
#
#[DEFAULT]
#library_dirs = /usr/local/lib
#include_dirs = /usr/local/include

# Atlas
# -----
# Atlas is an open source optimized implementation of the BLAS and Lapack
# routines. Numpy will try to build against Atlas by default when available in
# the system library dirs. To build numpy against a custom installation of
# Atlas you can add an explicit section such as the following. Here we assume
# that Atlas was configured with ``prefix=/opt/atlas``.
#
# [atlas]
# library_dirs = /opt/atlas/lib
# include_dirs = /opt/atlas/include

# OpenBLAS
# --------
# OpenBLAS is another open source optimized implementation of BLAS and Lapack
# and can be seen as an alternative to Atlas. To build numpy against OpenBLAS
# instead of Atlas, use this section instead of the above, adjusting as needed
# for your configuration (in the following example we installed OpenBLAS with
# ``make install PREFIX=/opt/OpenBLAS``.
#
# **Warning**: OpenBLAS, by default, is built in multithreaded mode. Due to the
# way Python's multiprocessing is implemented, a multithreaded OpenBLAS can
# cause programs using both to hang as soon as a worker process is forked on
# POSIX systems (Linux, Mac).
# This is fixed in Openblas 0.2.9 for the pthread build, the OpenMP build using
# GNU openmp is as of gcc-4.9 not fixed yet.
# Python 3.4 will introduce a new feature in multiprocessing, called the
# "forkserver", which solves this problem. For older versions, make sure
# OpenBLAS is built using pthreads or use Python threads instead of
# multiprocessing.
# (This problem does not exist with multithreaded ATLAS.)
#
# http://docs.python.org/3.4/library/multiprocessing.html#contexts-and-start-methods
# https://github.com/xianyi/OpenBLAS/issues/294
#
[openblas]
libraries = openblas
library_dirs = /usr/lib
include_dirs = /usr/include

# MKL
#----
# MKL is Intel's very optimized yet proprietary implementation of BLAS and
# Lapack.
# For recent (9.0.21, for example) mkl, you need to change the names of the
# lapack library. Assuming you installed the mkl in /opt, for a 32 bits cpu:
# [mkl]
# library_dirs = /opt/intel/mkl/9.1.023/lib/32/
# lapack_libs = mkl_lapack
#
# For 10.*, on 32 bits machines:
# [mkl]
# library_dirs = /opt/intel/mkl/10.0.1.014/lib/32/
# lapack_libs = mkl_lapack
# mkl_libs = mkl, guide

# UMFPACK
# -------
# The UMFPACK library is used in scikits.umfpack to factor large sparse matrices. 
# It, in turn, depends on the AMD library for reordering the matrices for
# better performance.  Note that the AMD library has nothing to do with AMD
# (Advanced Micro Devices), the CPU company.
#
# UMFPACK is not needed for numpy or scipy.
#
#   http://www.cise.ufl.edu/research/sparse/umfpack/
#   http://www.cise.ufl.edu/research/sparse/amd/
#   http://scikits.appspot.com/umfpack
#
#[amd]
#amd_libs = amd
#
#[umfpack]
#umfpack_libs = umfpack

# FFT libraries
# -------------
# There are two FFT libraries that we can configure here: FFTW (2 and 3) and djbfft.
# Note that these libraries are not needed for numpy or scipy.
#
#   http://fftw.org/
#   http://cr.yp.to/djbfft.html
#
# Given only this section, numpy.distutils will try to figure out which version
# of FFTW you are using.
#[fftw]
#libraries = fftw3
#
# For djbfft, numpy.distutils will look for either djbfft.a or libdjbfft.a . 
#[djbfft]
#include_dirs = /usr/local/djbfft/include
#library_dirs = /usr/local/djbfft/lib
-- 
2.1.0



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Re: [alpine-devel] [PATCH 2/2] testing/py-numpy: upgrade, use OpenBLAS

Natanael Copa <ncopa@alpinelinux.org>
Details
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<20140901095747.2748bb03@ncopa-desktop.alpinelinux.org>
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<1409264344-5879-2-git-send-email-ibid.ag@gmail.com> (view parent)
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On Thu, 28 Aug 2014 15:19:04 -0700
Isaac Dunham <ibid.ag@gmail.com> wrote:

> Upgraded to 1.8.1 so I could build with OpenBLAS.
> Fixed a typo while I was here.

both applied.

Thanks!

-nc


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