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Add new package: sgpp (#15961)

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* sgpp: Added recipe

* sgpp: Removed maintainer and updated patch

* sgpp: Added more conflicts

* sgpp: Added conflicts for older combigrid versions

* sgpp: Added one more maintainer

* sgpp: Add version 3.3.0 and sane defaults

* sgpp: Better description and c++11 conflicts

* sgpp: Updated maintainers

* sgpp: Fix flake8 errors

* sgpp: Fix dependencies and minor issues

- Added py-setuptools dependency
- Fixed zlib link dependency
- Added git url
- Using spec.satisfies where appropriate

* sgpp: Added testing to package

* sgpp: Remove simd variant and use spec instead

* sgpp: Remove java variant

* sgpp: Small bugfixes

* sgpp: Add datadriven patch and patch explanations
This commit is contained in:
Gregor Daiß 2020-04-21 23:03:46 +02:00 committed by GitHub
parent f1050c4be2
commit 745804582b
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GPG Key ID: 4AEE18F83AFDEB23
5 changed files with 421 additions and 0 deletions
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21
var/spack/repos/builtin/packages/sgpp/avx512_datadriven_compilation.patch Normal file
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diff --git a/datadriven/src/sgpp/datadriven/operation/hash/OperationMultiEvalStreaming/OperationMultiEvalStreaming_multImpl.cpp b/datadriven/src/sgpp/datadriven/operation/hash/OperationMultiEvalStreaming/OperationMultiEvalStreaming_multImpl.cpp
index 7fafd43d4..ea15ba137 100644
--- a/datadriven/src/sgpp/datadriven/operation/hash/OperationMultiEvalStreaming/OperationMultiEvalStreaming_multImpl.cpp
+++ b/datadriven/src/sgpp/datadriven/operation/hash/OperationMultiEvalStreaming/OperationMultiEvalStreaming_multImpl.cpp
@@ -295,6 +295,7 @@ void OperationMultiEvalStreaming::multImpl(
_mm512_extload_pd(A, _MM_UPCONV_PD_NONE, _MM_BROADCAST_1X8, _MM_HINT_NONE)
#define _mm512_max_pd(A, B) _mm512_gmax_pd(A, B)
#define _mm512_set1_epi64(A) _mm512_set_1to8_epi64(A)
+#define _mm512_set1_pd(A) _mm512_set_1to8_pd(A)
#endif
#if defined(__AVX512F__)
#define _mm512_broadcast_sd(A) _mm512_broadcastsd_pd(_mm_load_sd(A))
@@ -409,7 +410,7 @@ void OperationMultiEvalStreaming::multImpl(
eval_11 = _mm512_castsi512_pd(_mm512_and_epi64(abs2Mask, _mm512_castpd_si512(eval_11)));
#endif
- __m512d one = _mm512_set_1to8_pd(1.0);
+ __m512d one = _mm512_set1_pd(1.0);
eval_0 = _mm512_sub_pd(one, eval_0);
eval_1 = _mm512_sub_pd(one, eval_1);

22
var/spack/repos/builtin/packages/sgpp/directory.patch Normal file
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@ -0,0 +1,22 @@
diff --git a/SConstruct b/SConstruct
index 98c1a56ac..30baef5e5 100644
--- a/SConstruct
+++ b/SConstruct
@@ -293,7 +293,7 @@ Parameters are:
for line in vars.GenerateHelpText(env).splitlines()]))
# add trailing slashes were required and if not present
-BUILD_DIR = Dir(os.path.join("lib", "sgpp"))
+BUILD_DIR = Dir(os.path.join("lib"))
Export("BUILD_DIR")
PYSGPP_PACKAGE_PATH = Dir(os.path.join("lib"))
Export("PYSGPP_PACKAGE_PATH")
@@ -550,7 +550,7 @@ env.SideEffect("sideEffectFinalSteps", exampleTargetList)
#########################################################################
installLibSGpp = env.Alias("install-lib-sgpp",
- env.Install(os.path.join(env.get("LIBDIR"), "sgpp"),
+ env.Install(os.path.join(env.get("LIBDIR")),
libraryTargetList))
headerFinalDestList = []

160
var/spack/repos/builtin/packages/sgpp/fix-setup-py.patch Normal file
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@ -0,0 +1,160 @@
diff --git a/setup.py b/setup.py
index af1ec083e..d971f87c5 100644
--- a/setup.py
+++ b/setup.py
@@ -1,5 +1,5 @@
-#!/usr/bin/env python
-# Copyright (C) 2008-today The SG++ Project
+#!/usr/bin/env python
+# Copyright (C) 2008-today The SG++ project
# This file is part of the SG++ project. For conditions of distribution and
# use, please see the copyright notice provided with SG++ or at
# sgpp.sparsegrids.org
@@ -8,17 +8,26 @@
# script creates a pysgpp lib in the site-packages of
# python. Furthermore, it collects all the relevant python code,
# located in each module under the path <module name>/python and
-# copies it to the site-package folder of pysgpp using the following
-# scheme: <path to site-packages>/pysgpp-<unique
-# key>/extensions/<module name>/<copy of python code of correponding
-# module>.
+# copies it to the site-package folder of pysgpp under the extensions namespace
+# pysgpp.extensions
import os
import shutil
-from setuptools import setup
+from setuptools import setup, find_packages
+
+
+try:
+ from wheel.bdist_wheel import bdist_wheel as _bdist_wheel
+ class bdist_wheel(_bdist_wheel):
+ def finalize_options(self):
+ _bdist_wheel.finalize_options(self)
+ self.root_is_pure = False
+except ImportError:
+ bdist_wheel = None
# path to pysgpp lib
libpath = os.path.join("lib", "pysgpp")
+extensionspath = os.path.join(libpath, "extensions")
# list of all available modules -> all folders in the root directory
moduleFolders = [filename for filename in os.listdir(".")
@@ -29,16 +38,44 @@ pythonModuleFolders = [(moduleFolder, os.path.join(moduleFolder, "python"))
for moduleFolder in moduleFolders
if os.path.exists(os.path.join(moduleFolder, "python"))]
-# create the data file list such that it can be used by setuptools
-dataFiles = []
+try:
+ os.mkdir(extensionspath)
+except FileExistsError as e:
+ pass
+
+# create list of extension scripts
+extFiles = []
for moduleFolder, srcdir in pythonModuleFolders:
- basepath = os.path.join("pysgpp", "extensions", moduleFolder)
+ basepath = os.path.join(extensionspath, moduleFolder)
+ try:
+ os.mkdir(basepath)
+ except FileExistsError as e:
+ pass
for root, dirs, files in os.walk(srcdir):
- if '.svn' in dirs:
- dirs.remove('.svn')
+ if '.git' in dirs:
+ dirs.remove('.git')
+
+ extFiles += [os.path.join(root, f) for f in files if ".py" in f]
+
+##
+# copy extension python files to new layout
+# pysgpp
+# --extensions
+# ----modulename
+# ------*.py
+##
- dataFiles += [(root.replace(srcdir, basepath),
- [os.path.join(root, f) for f in files])]
+for f in extFiles:
+ dest = os.path.join(extensionspath,f)
+ dest = dest.replace(os.sep + "python", "")
+ try:
+ shutil.copy2(f, dest)
+ except FileNotFoundError as e:
+ os.mkdir(os.path.dirname(dest))
+ shutil.copy2(f, dest)
+ except shutil.SameFileError as e:
+ pass
+
# write init file for pysgpp
initFile = os.path.join(libpath, "__init__.py")
@@ -50,8 +87,8 @@ import sys
sys.path.append(os.path.dirname(__file__))
# import pysgpp_swig and extensions
-from pysgpp_swig import *
-import pysgpp.extensions
+from .pysgpp_swig import *
+from . import extensions
""")
if len(moduleFolders) > 0:
@@ -59,9 +96,13 @@ if len(moduleFolders) > 0:
initFile = os.path.join("__init__.py")
with open(initFile, "w") as f:
for moduleFolder, _ in pythonModuleFolders:
- f.write("import %s\n" % moduleFolder)
+ f.write("from . import %s\n" % moduleFolder)
- dataFiles += [(os.path.join("pysgpp", "extensions"), [initFile])]
+ try:
+ shutil.copy2(initFile, os.path.join(extensionspath, initFile))
+ except shutil.SameFileError as e:
+ pass
+
# if the current system is windows we need to rename the dll to pyd
dllLibs = [filename for filename in os.listdir(libpath)
@@ -74,20 +115,27 @@ for dllLib in dllLibs:
# setup pysgpp
setup(name='pysgpp',
- version="1.0.0",
- url='sgpp.sparsegrids.org',
- author="Fabian Franzelin",
- description='',
- license='',
+ version="0.0.0",
+ url='https://github.com/SGpp/SGpp',
+ author="Dirk.Pflueger@ipvs.uni-stuttgart.de",
+ description='''The sparse grids toolkit SG++
+ SG++ is a collection of numerical algorithms for sparse grids. It
+ contains modules for interpolation, quadrature, data mining
+ (regression, classification, clustering), optimization, PDEs, and
+ more. SG++ implements algorithms for spatially adaptive grids and
+ also provides a module for the combination technique. Many of the
+ implemented algorithms are also available as a high-performance
+ version, often orders of magnitude faster than standard
+ implementations.''',
+ license='BSD-style license',
long_description="README",
- platforms='any',
zip_safe=False,
package_dir={'': 'lib'},
- packages=['pysgpp'],
- package_data={'pysgpp': ['*.so', '*.lib', '*.pyd']},
- data_files=dataFiles
+ packages=find_packages(where='lib', include=['pysgpp', 'pysgpp.extensions*']),
+ package_data={'pysgpp': ['_pysgpp_swig.so', '*.lib', '*.pyd']},
)
# cleanup
if len(moduleFolders) > 0 and os.path.exists(initFile):
os.remove(initFile)
+ shutil.rmtree(extensionspath, ignore_errors=True)

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var/spack/repos/builtin/packages/sgpp/ocl.patch Normal file
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diff --git a/datadriven/examplesOCL/multiEvalPerformance.cpp b/datadriven/examplesOCL/multiEvalPerformance.cpp
index 60c281353..373e8509d 100644
--- a/datadriven/examplesOCL/multiEvalPerformance.cpp
+++ b/datadriven/examplesOCL/multiEvalPerformance.cpp
@@ -17,7 +17,7 @@ int main(int argc, char** argv) {
std::string fileName = "debugging.arff";
sgpp::datadriven::ARFFTools arffTools;
- sgpp::datadriven::Dataset dataset = arffTools.readARFFFromeFile(fileName);
+ sgpp::datadriven::Dataset dataset = arffTools.readARFFFromFile(fileName);
// sgpp::base::DataVector *classes = dataset.getClasses();
sgpp::base::DataMatrix& trainingData = dataset.getData();

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# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class Sgpp(SConsPackage):
"""SGpp is a library and framework for sparse grids in different flavors.
SGpp supports both hierarchical spatially-adaptive sparse grids and the
dimensionally-adaptive sparse grid combination technique."""
homepage = "https://sgpp.sparsegrids.org"
url = "https://github.com/SGpp/SGpp/archive/v3.2.0.tar.gz"
git = "https://github.com/SGpp/SGpp.git"
maintainers = ['G-071', 'leiterrl', 'pfluegdk']
# Versions with Python 3 bindings:
version('master', branch='master')
version('3.3.0', sha256='ca4d5b79f315b425ce69b04940c141451a76848bf1bd7b96067217304c68e2d4')
version('3.2.0', sha256='dab83587fd447f92ed8546eacaac6b8cbe65b8db5e860218c0fa2e42f776962d')
# Versions with Python 2 bindings:
version('3.1.0', sha256='6b46bc5b3966e92567d6754130666bdffb7be1d1d2c1b427d7ce964b8eaab526')
version('3.0.0', sha256='4dd9049e664abd7db78c355fea5e192167812f443115d4bf686a51bb1e9bda9c')
# Patches with bugfixes that are necessary to build old SGpp versions
# with spack. Patches are submitted upstream, but need to applied
# for versions too old to include them as they will not be
# backported for old releases:
# Patch that ensures libraries will actually
# be copied into prefix/lib upon installation
# (otherwise it would be prefix/lib/sgpp)
# Fixed in SGpp in PR https://github.com/SGpp/SGpp/pull/222
patch('directory.patch', when='@:3.2.0')
# Fix faulty setup.py introduced in 3.2.0
# Fixed in SGpp in version 3.3.0
patch('fix-setup-py.patch', when='@3.2.0')
# Fix compilation issue with opencl introduced in 3.2.0
# Fixed in SGpp in PR https://github.com/SGpp/SGpp/pull/219
patch('ocl.patch', when='@3.2.0+opencl')
# Fixes compilation with AVX512 and datadriven
# Fixed in SGpp in PR https://github.com/SGpp/SGpp/pull/229
patch('avx512_datadriven_compilation.patch', when='@:3.3.0+datadriven')
variant('python', default=True,
description='Provide Python bindings for SGpp')
variant('optimization', default=True,
description='Builds the optimization module of SGpp')
variant('pde', default=True,
description='Builds the datadriven module of SGpp')
variant('quadrature', default=True,
description='Builds the datadriven module of SGpp')
variant('datadriven', default=False,
description='Builds the datadriven module of SGpp')
variant('misc', default=False,
description='Builds the misc module of SGpp')
variant('combigrid', default=False,
description='Builds the combigrid module of SGpp')
variant('solver', default=True,
description='Builds the solver module of SGpp')
variant('opencl', default=False,
description='Enables support for OpenCL accelerated operations')
variant('mpi', default=False,
description='Enables support for MPI-distributed operations')
# Java variant deactivated due to spack issue #987
# variant('java', default=False,
# description='Provide Java bindings for SGpp')
# depends_on('swig@3:', when='+java', type=('build'))
# extends('openjdk', when='+java')
# Mandatory dependencies
depends_on('scons@2.5.1', when='@:3.1.0', type=('build'))
depends_on('scons@3:', when='@3.2.0:', type=('build'))
depends_on('zlib', type=('link'))
# Python dependencies
extends('python', when='+python')
depends_on('py-setuptools', when='+python', type=('build'))
# Python 3 support was added in version 3.2.0
depends_on('python@2.7:2.8', when='@:3.1.0+python', type=('build', 'run'))
depends_on('python@3:', when='@3.2.0:+python', type=('build', 'run'))
depends_on('swig@3:', when='+python', type=('build'))
# Python libraries (version depends on whether we use Python 2 or 3)
depends_on('py-numpy@:1.16', when='@:3.1.0+python', type=('build', 'run'))
depends_on('py-numpy@1.17:', when='@3.2.0:+python', type=('build', 'run'))
depends_on('py-scipy@:1.2.3', when='@:3.1.0+python', type=('build', 'run'))
depends_on('py-scipy@1.3.0:', when='@3.2.0:+python', type=('build', 'run'))
# OpenCL dependency
depends_on('opencl@1.1:', when='+opencl', type=('build', 'run'))
# MPI dependency
depends_on('mpi', when='+mpi', type=('build', 'run'))
# Testing requires boost test
depends_on('boost+test', type=('test'))
# Compiler with C++11 support is required
conflicts('%gcc@:4.8.4', msg='Compiler with c++11 support is required!')
conflicts('%clang@:3.2', msg='Compiler with c++11 support is required!')
conflicts('%intel@:14', msg='Compiler with c++11 support is required!')
# Solver python bindings are actually using the pde module at one point:
conflicts('-pde', when='+python+solver')
# some modules depend on each other (notably datadriven and misc)
conflicts('+pde', when='-solver')
# Datadriven module requirements
conflicts('+datadriven', when='-solver')
conflicts('+datadriven', when='-optimization')
conflicts('+datadriven', when='-pde')
# Misc module requirements
conflicts('+misc', when='-datadriven')
conflicts('+misc', when='-solver')
conflicts('+misc', when='-optimization')
conflicts('+misc', when='-pde')
conflicts('+misc', when='@:3.1.0',
msg='The misc module was introduced in version 3.2.0')
# Combigrid module requirements (for 3.2.0 or older)
# newer combigrids have no dependencies
conflicts('+combigrid', when='@:3.2.0~optimization')
conflicts('+combigrid', when='@:3.2.0~pde')
conflicts('+combigrid', when='@:3.2.0~solver')
conflicts('+combigrid', when='@:3.2.0~quadrature')
def build_args(self, spec, prefix):
# Testing parameters
if self.run_tests:
self.args = ['COMPILE_BOOST_TESTS=1',
'RUN_BOOST_TESTS=1']
if ('+python' in spec):
self.args.append('RUN_PYTHON_TESTS=1')
if spec.satisfies('@:3.2.0'):
self.args.append('RUN_CPPLINT=1')
else: # argument was renamed after 3.2.0
self.args.append('CHECK_STYLE=1')
else:
self.args = ['COMPILE_BOOST_TESTS=0',
'RUN_BOOST_TESTS=0',
'RUN_PYTHON_TESTS=0']
if spec.satisfies('@:3.2.0'):
self.args.append('RUN_CPPLINT=0')
else: # argument was renamed after 3.2.0
self.args.append('CHECK_STYLE=0')
# Install direction
self.args.append('PREFIX={0}'.format(prefix))
# Generate swig bindings?
self.args.append('SG_PYTHON={0}'.format(
'1' if '+python' in spec else '0'))
# Java variant deactivated due to spack issue #987
# self.args.append('SG_JAVA={0}'.format(
# '1' if '+java' in spec else '0'))
self.args.append('SG_JAVA=0')
# Which modules to build?
self.args.append('SG_OPTIMIZATION={0}'.format(
'1' if '+optimization' in spec else '0'))
self.args.append('SG_QUADRATURE={0}'.format(
'1' if '+quadrature' in spec else '0'))
self.args.append('SG_PDE={0}'.format(
'1' if '+pde' in spec else '0'))
self.args.append('SG_DATADRIVEN={0}'.format(
'1' if '+datadriven' in spec else '0'))
self.args.append('SG_COMBIGRID={0}'.format(
'1' if '+combigrid' in spec else '0'))
self.args.append('SG_SOLVER={0}'.format(
'1' if '+solver' in spec else '0'))
# Misc flag did not exist in older versions
if spec.satisfies('@3.2.0:'):
self.args.append('SG_MISC={0}'.format(
'1' if '+misc' in spec else '0'))
# SIMD scons parameter (pick according to simd spec)
if 'avx512' in self.spec.target:
self.args.append('ARCH=avx512')
elif 'avx2' in self.spec.target:
self.args.append('ARCH=avx2')
elif 'avx' in self.spec.target:
self.args.append('ARCH=avx')
elif 'fma4' in self.spec.target:
self.args.append('ARCH=fma4')
elif 'sse42' in self.spec.target:
self.args.append('ARCH=sse42')
elif 'sse3' in self.spec.target:
self.args.append('ARCH=sse3')
# OpenCL Flags
self.args.append('USE_OCL={0}'.format(
'1' if '+opencl' in spec else '0'))
# Get the mpicxx compiler from the Spack spec
# (makes certain we use the one from spack):
if ('+mpi' in spec):
self.args.append('CXX={0}'.format(
self.spec['mpi'].mpicxx))
return self.args
def install_args(self, spec, prefix):
# Everything is already built, time to install our python bindings:
if '+python' in spec:
setup_py('install', '--prefix={0}'.format(prefix))
return self.args