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authorGregor Daiß <G-071@users.noreply.github.com>2020-04-21 23:03:46 +0200
committerGitHub <noreply@github.com>2020-04-21 16:03:46 -0500
commit745804582be4c8ef25ba9b0cb7dee62aa6e4b8a7 (patch)
treea9e8857d473f52228b08cb1a945b84a1520d719c
parentf1050c4be2954db88342f052f24326fb3017b7e0 (diff)
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Add new package: sgpp (#15961)
* 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
-rw-r--r--var/spack/repos/builtin/packages/sgpp/avx512_datadriven_compilation.patch21
-rw-r--r--var/spack/repos/builtin/packages/sgpp/directory.patch22
-rw-r--r--var/spack/repos/builtin/packages/sgpp/fix-setup-py.patch160
-rw-r--r--var/spack/repos/builtin/packages/sgpp/ocl.patch13
-rw-r--r--var/spack/repos/builtin/packages/sgpp/package.py205
5 files changed, 421 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/sgpp/avx512_datadriven_compilation.patch b/var/spack/repos/builtin/packages/sgpp/avx512_datadriven_compilation.patch
new file mode 100644
index 0000000000..268cba6358
--- /dev/null
+++ b/var/spack/repos/builtin/packages/sgpp/avx512_datadriven_compilation.patch
@@ -0,0 +1,21 @@
+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);
diff --git a/var/spack/repos/builtin/packages/sgpp/directory.patch b/var/spack/repos/builtin/packages/sgpp/directory.patch
new file mode 100644
index 0000000000..f1b2286423
--- /dev/null
+++ b/var/spack/repos/builtin/packages/sgpp/directory.patch
@@ -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 = []
diff --git a/var/spack/repos/builtin/packages/sgpp/fix-setup-py.patch b/var/spack/repos/builtin/packages/sgpp/fix-setup-py.patch
new file mode 100644
index 0000000000..e201a5dff0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/sgpp/fix-setup-py.patch
@@ -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)
diff --git a/var/spack/repos/builtin/packages/sgpp/ocl.patch b/var/spack/repos/builtin/packages/sgpp/ocl.patch
new file mode 100644
index 0000000000..fbdca6ff18
--- /dev/null
+++ b/var/spack/repos/builtin/packages/sgpp/ocl.patch
@@ -0,0 +1,13 @@
+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();
diff --git a/var/spack/repos/builtin/packages/sgpp/package.py b/var/spack/repos/builtin/packages/sgpp/package.py
new file mode 100644
index 0000000000..7e5b907374
--- /dev/null
+++ b/var/spack/repos/builtin/packages/sgpp/package.py
@@ -0,0 +1,205 @@
+# 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