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

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