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
This commit is contained in:
Gregor Daiß
GitHub
parent
f1050c4be2
commit
745804582b
@ -0,0 +1,21 @@
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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
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index 7fafd43d4..ea15ba137 100644
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--- a/datadriven/src/sgpp/datadriven/operation/hash/OperationMultiEvalStreaming/OperationMultiEvalStreaming_multImpl.cpp
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+++ b/datadriven/src/sgpp/datadriven/operation/hash/OperationMultiEvalStreaming/OperationMultiEvalStreaming_multImpl.cpp
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@@ -295,6 +295,7 @@ void OperationMultiEvalStreaming::multImpl(
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_mm512_extload_pd(A, _MM_UPCONV_PD_NONE, _MM_BROADCAST_1X8, _MM_HINT_NONE)
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#define _mm512_max_pd(A, B) _mm512_gmax_pd(A, B)
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#define _mm512_set1_epi64(A) _mm512_set_1to8_epi64(A)
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+#define _mm512_set1_pd(A) _mm512_set_1to8_pd(A)
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#endif
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#if defined(__AVX512F__)
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#define _mm512_broadcast_sd(A) _mm512_broadcastsd_pd(_mm_load_sd(A))
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@@ -409,7 +410,7 @@ void OperationMultiEvalStreaming::multImpl(
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eval_11 = _mm512_castsi512_pd(_mm512_and_epi64(abs2Mask, _mm512_castpd_si512(eval_11)));
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#endif
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- __m512d one = _mm512_set_1to8_pd(1.0);
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+ __m512d one = _mm512_set1_pd(1.0);
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eval_0 = _mm512_sub_pd(one, eval_0);
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eval_1 = _mm512_sub_pd(one, eval_1);
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22
var/spack/repos/builtin/packages/sgpp/directory.patch
Normal file
22
var/spack/repos/builtin/packages/sgpp/directory.patch
Normal file
@ -0,0 +1,22 @@
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diff --git a/SConstruct b/SConstruct
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index 98c1a56ac..30baef5e5 100644
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--- a/SConstruct
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+++ b/SConstruct
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@@ -293,7 +293,7 @@ Parameters are:
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for line in vars.GenerateHelpText(env).splitlines()]))
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# add trailing slashes were required and if not present
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-BUILD_DIR = Dir(os.path.join("lib", "sgpp"))
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+BUILD_DIR = Dir(os.path.join("lib"))
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Export("BUILD_DIR")
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PYSGPP_PACKAGE_PATH = Dir(os.path.join("lib"))
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Export("PYSGPP_PACKAGE_PATH")
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@@ -550,7 +550,7 @@ env.SideEffect("sideEffectFinalSteps", exampleTargetList)
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#########################################################################
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installLibSGpp = env.Alias("install-lib-sgpp",
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- env.Install(os.path.join(env.get("LIBDIR"), "sgpp"),
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+ env.Install(os.path.join(env.get("LIBDIR")),
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libraryTargetList))
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headerFinalDestList = []
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160
var/spack/repos/builtin/packages/sgpp/fix-setup-py.patch
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160
var/spack/repos/builtin/packages/sgpp/fix-setup-py.patch
Normal file
@ -0,0 +1,160 @@
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diff --git a/setup.py b/setup.py
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index af1ec083e..d971f87c5 100644
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--- a/setup.py
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+++ b/setup.py
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@@ -1,5 +1,5 @@
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-#!/usr/bin/env python
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-# Copyright (C) 2008-today The SG++ Project
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+#!/usr/bin/env python
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+# Copyright (C) 2008-today The SG++ project
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# This file is part of the SG++ project. For conditions of distribution and
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# use, please see the copyright notice provided with SG++ or at
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# sgpp.sparsegrids.org
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@@ -8,17 +8,26 @@
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# script creates a pysgpp lib in the site-packages of
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# python. Furthermore, it collects all the relevant python code,
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# located in each module under the path <module name>/python and
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-# copies it to the site-package folder of pysgpp using the following
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-# scheme: <path to site-packages>/pysgpp-<unique
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-# key>/extensions/<module name>/<copy of python code of correponding
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-# module>.
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+# copies it to the site-package folder of pysgpp under the extensions namespace
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+# pysgpp.extensions
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import os
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import shutil
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-from setuptools import setup
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+from setuptools import setup, find_packages
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+
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+
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+try:
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+ from wheel.bdist_wheel import bdist_wheel as _bdist_wheel
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+ class bdist_wheel(_bdist_wheel):
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+ def finalize_options(self):
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+ _bdist_wheel.finalize_options(self)
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+ self.root_is_pure = False
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+except ImportError:
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+ bdist_wheel = None
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# path to pysgpp lib
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libpath = os.path.join("lib", "pysgpp")
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+extensionspath = os.path.join(libpath, "extensions")
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# list of all available modules -> all folders in the root directory
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moduleFolders = [filename for filename in os.listdir(".")
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@@ -29,16 +38,44 @@ pythonModuleFolders = [(moduleFolder, os.path.join(moduleFolder, "python"))
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for moduleFolder in moduleFolders
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if os.path.exists(os.path.join(moduleFolder, "python"))]
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-# create the data file list such that it can be used by setuptools
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-dataFiles = []
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+try:
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+ os.mkdir(extensionspath)
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+except FileExistsError as e:
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+ pass
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+
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+# create list of extension scripts
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+extFiles = []
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for moduleFolder, srcdir in pythonModuleFolders:
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- basepath = os.path.join("pysgpp", "extensions", moduleFolder)
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+ basepath = os.path.join(extensionspath, moduleFolder)
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+ try:
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+ os.mkdir(basepath)
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+ except FileExistsError as e:
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+ pass
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for root, dirs, files in os.walk(srcdir):
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- if '.svn' in dirs:
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- dirs.remove('.svn')
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+ if '.git' in dirs:
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+ dirs.remove('.git')
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+
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+ extFiles += [os.path.join(root, f) for f in files if ".py" in f]
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+
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+##
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+# copy extension python files to new layout
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+# pysgpp
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+# --extensions
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+# ----modulename
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+# ------*.py
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+##
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- dataFiles += [(root.replace(srcdir, basepath),
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- [os.path.join(root, f) for f in files])]
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+for f in extFiles:
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+ dest = os.path.join(extensionspath,f)
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+ dest = dest.replace(os.sep + "python", "")
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+ try:
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+ shutil.copy2(f, dest)
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+ except FileNotFoundError as e:
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+ os.mkdir(os.path.dirname(dest))
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+ shutil.copy2(f, dest)
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+ except shutil.SameFileError as e:
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+ pass
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+
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# write init file for pysgpp
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initFile = os.path.join(libpath, "__init__.py")
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@@ -50,8 +87,8 @@ import sys
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sys.path.append(os.path.dirname(__file__))
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# import pysgpp_swig and extensions
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-from pysgpp_swig import *
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-import pysgpp.extensions
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+from .pysgpp_swig import *
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+from . import extensions
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""")
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if len(moduleFolders) > 0:
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@@ -59,9 +96,13 @@ if len(moduleFolders) > 0:
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initFile = os.path.join("__init__.py")
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with open(initFile, "w") as f:
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for moduleFolder, _ in pythonModuleFolders:
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- f.write("import %s\n" % moduleFolder)
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+ f.write("from . import %s\n" % moduleFolder)
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- dataFiles += [(os.path.join("pysgpp", "extensions"), [initFile])]
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+ try:
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+ shutil.copy2(initFile, os.path.join(extensionspath, initFile))
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+ except shutil.SameFileError as e:
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+ pass
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+
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# if the current system is windows we need to rename the dll to pyd
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dllLibs = [filename for filename in os.listdir(libpath)
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@@ -74,20 +115,27 @@ for dllLib in dllLibs:
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# setup pysgpp
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setup(name='pysgpp',
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- version="1.0.0",
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- url='sgpp.sparsegrids.org',
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- author="Fabian Franzelin",
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- description='',
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- license='',
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+ version="0.0.0",
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+ url='https://github.com/SGpp/SGpp',
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+ author="Dirk.Pflueger@ipvs.uni-stuttgart.de",
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+ description='''The sparse grids toolkit SG++
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+ SG++ is a collection of numerical algorithms for sparse grids. It
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+ contains modules for interpolation, quadrature, data mining
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+ (regression, classification, clustering), optimization, PDEs, and
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+ more. SG++ implements algorithms for spatially adaptive grids and
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+ also provides a module for the combination technique. Many of the
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+ implemented algorithms are also available as a high-performance
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+ version, often orders of magnitude faster than standard
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+ implementations.''',
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+ license='BSD-style license',
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long_description="README",
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- platforms='any',
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zip_safe=False,
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package_dir={'': 'lib'},
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- packages=['pysgpp'],
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- package_data={'pysgpp': ['*.so', '*.lib', '*.pyd']},
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- data_files=dataFiles
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+ packages=find_packages(where='lib', include=['pysgpp', 'pysgpp.extensions*']),
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+ package_data={'pysgpp': ['_pysgpp_swig.so', '*.lib', '*.pyd']},
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)
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# cleanup
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if len(moduleFolders) > 0 and os.path.exists(initFile):
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os.remove(initFile)
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+ shutil.rmtree(extensionspath, ignore_errors=True)
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13
var/spack/repos/builtin/packages/sgpp/ocl.patch
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13
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
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index 60c281353..373e8509d 100644
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--- a/datadriven/examplesOCL/multiEvalPerformance.cpp
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+++ b/datadriven/examplesOCL/multiEvalPerformance.cpp
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@@ -17,7 +17,7 @@ int main(int argc, char** argv) {
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std::string fileName = "debugging.arff";
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sgpp::datadriven::ARFFTools arffTools;
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- sgpp::datadriven::Dataset dataset = arffTools.readARFFFromeFile(fileName);
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+ sgpp::datadriven::Dataset dataset = arffTools.readARFFFromFile(fileName);
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// sgpp::base::DataVector *classes = dataset.getClasses();
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sgpp::base::DataMatrix& trainingData = dataset.getData();
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205
var/spack/repos/builtin/packages/sgpp/package.py
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205
var/spack/repos/builtin/packages/sgpp/package.py
Normal file
@ -0,0 +1,205 @@
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# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
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# Spack Project Developers. See the top-level COPYRIGHT file for details.
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#
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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from spack import *
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class Sgpp(SConsPackage):
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"""SGpp is a library and framework for sparse grids in different flavors.
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SGpp supports both hierarchical spatially-adaptive sparse grids and the
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dimensionally-adaptive sparse grid combination technique."""
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homepage = "https://sgpp.sparsegrids.org"
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url = "https://github.com/SGpp/SGpp/archive/v3.2.0.tar.gz"
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git = "https://github.com/SGpp/SGpp.git"
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maintainers = ['G-071', 'leiterrl', 'pfluegdk']
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# Versions with Python 3 bindings:
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version('master', branch='master')
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version('3.3.0', sha256='ca4d5b79f315b425ce69b04940c141451a76848bf1bd7b96067217304c68e2d4')
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version('3.2.0', sha256='dab83587fd447f92ed8546eacaac6b8cbe65b8db5e860218c0fa2e42f776962d')
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# Versions with Python 2 bindings:
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version('3.1.0', sha256='6b46bc5b3966e92567d6754130666bdffb7be1d1d2c1b427d7ce964b8eaab526')
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version('3.0.0', sha256='4dd9049e664abd7db78c355fea5e192167812f443115d4bf686a51bb1e9bda9c')
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# Patches with bugfixes that are necessary to build old SGpp versions
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# with spack. Patches are submitted upstream, but need to applied
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# for versions too old to include them as they will not be
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# backported for old releases:
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# Patch that ensures libraries will actually
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# be copied into prefix/lib upon installation
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# (otherwise it would be prefix/lib/sgpp)
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# Fixed in SGpp in PR https://github.com/SGpp/SGpp/pull/222
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patch('directory.patch', when='@:3.2.0')
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# Fix faulty setup.py introduced in 3.2.0
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# Fixed in SGpp in version 3.3.0
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patch('fix-setup-py.patch', when='@3.2.0')
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# Fix compilation issue with opencl introduced in 3.2.0
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# Fixed in SGpp in PR https://github.com/SGpp/SGpp/pull/219
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patch('ocl.patch', when='@3.2.0+opencl')
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# Fixes compilation with AVX512 and datadriven
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# Fixed in SGpp in PR https://github.com/SGpp/SGpp/pull/229
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patch('avx512_datadriven_compilation.patch', when='@:3.3.0+datadriven')
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variant('python', default=True,
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description='Provide Python bindings for SGpp')
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variant('optimization', default=True,
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description='Builds the optimization module of SGpp')
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variant('pde', default=True,
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description='Builds the datadriven module of SGpp')
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variant('quadrature', default=True,
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description='Builds the datadriven module of SGpp')
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variant('datadriven', default=False,
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description='Builds the datadriven module of SGpp')
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variant('misc', default=False,
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description='Builds the misc module of SGpp')
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variant('combigrid', default=False,
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description='Builds the combigrid module of SGpp')
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variant('solver', default=True,
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description='Builds the solver module of SGpp')
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variant('opencl', default=False,
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description='Enables support for OpenCL accelerated operations')
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variant('mpi', default=False,
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description='Enables support for MPI-distributed operations')
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# Java variant deactivated due to spack issue #987
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# variant('java', default=False,
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# description='Provide Java bindings for SGpp')
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# depends_on('swig@3:', when='+java', type=('build'))
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# extends('openjdk', when='+java')
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# Mandatory dependencies
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depends_on('scons@2.5.1', when='@:3.1.0', type=('build'))
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depends_on('scons@3:', when='@3.2.0:', type=('build'))
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depends_on('zlib', type=('link'))
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# Python dependencies
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extends('python', when='+python')
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depends_on('py-setuptools', when='+python', type=('build'))
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# Python 3 support was added in version 3.2.0
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depends_on('python@2.7:2.8', when='@:3.1.0+python', type=('build', 'run'))
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depends_on('python@3:', when='@3.2.0:+python', type=('build', 'run'))
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depends_on('swig@3:', when='+python', type=('build'))
|
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# Python libraries (version depends on whether we use Python 2 or 3)
|
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depends_on('py-numpy@:1.16', when='@:3.1.0+python', type=('build', 'run'))
|
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depends_on('py-numpy@1.17:', when='@3.2.0:+python', type=('build', 'run'))
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depends_on('py-scipy@:1.2.3', when='@:3.1.0+python', type=('build', 'run'))
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depends_on('py-scipy@1.3.0:', when='@3.2.0:+python', type=('build', 'run'))
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# OpenCL dependency
|
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depends_on('opencl@1.1:', when='+opencl', type=('build', 'run'))
|
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# MPI dependency
|
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depends_on('mpi', when='+mpi', type=('build', 'run'))
|
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# Testing requires boost test
|
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depends_on('boost+test', type=('test'))
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# Compiler with C++11 support is required
|
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conflicts('%gcc@:4.8.4', msg='Compiler with c++11 support is required!')
|
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conflicts('%clang@:3.2', msg='Compiler with c++11 support is required!')
|
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conflicts('%intel@:14', msg='Compiler with c++11 support is required!')
|
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# Solver python bindings are actually using the pde module at one point:
|
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conflicts('-pde', when='+python+solver')
|
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# 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')
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||||
conflicts('+combigrid', when='@:3.2.0~pde')
|
||||
conflicts('+combigrid', when='@:3.2.0~solver')
|
||||
conflicts('+combigrid', when='@:3.2.0~quadrature')
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||||
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
|
||||
Loading…
Reference in New Issue
Block a user