diff --git a/Jenkinsfile b/Jenkinsfile
index 1ace2a79..a7e7eb3a 100644
--- a/Jenkinsfile
+++ b/Jenkinsfile
@@ -1,119 +1,120 @@
pipeline {
parameters {string(defaultValue: '', description: 'api-token', name: 'API_TOKEN')
string(defaultValue: '', description: 'Token for readthedocs', name: 'RTD_TOKEN')
string(defaultValue: '', description: 'buildable phid', name: 'BUILD_TARGET_PHID')
string(defaultValue: '', description: 'Commit id', name: 'COMMIT_ID')
string(defaultValue: '', description: 'Diff id', name: 'DIFF_ID')
string(defaultValue: 'PHID-PROJ-gbo56hpf2y5bi7t5jusk', description: 'ID of the project', name: 'PROJECT_ID')
}
environment {
PHABRICATOR_HOST = 'https://c4science.ch/api/'
PYTHONPATH = sh returnStdout: true, script: 'echo ${WORKSPACE}/tests/ci/script/'
}
agent {
dockerfile { additionalBuildArgs '--tag tamaas-environment'}
}
stages {
stage('SCM Checkout') {
steps {
checkout scm: [
$class: 'GitSCM',
branches: scm.branches,
extensions: [[
$class: 'SubmoduleOption',
recursiveSubmodules: true,
]],
userRemoteConfigs: scm.userRemoteConfigs
]
}
}
stage('Configure') {
steps {
sh '''#!/usr/bin/env bash
echo "py_exec = \'python3\'" > build-setup.conf
echo "build_python = \'true\'" >> build-setup.conf
echo "build_tests = \'true\'" >> build-setup.conf
echo "use_googletest = \'true\'" >> build-setup.conf
- echo "use_mpi = \'true\'" >> build-setup.conf'''
+ echo "use_mpi = \'true\'" >> build-setup.conf
+ echo "verbose = \'true\'" >> build-setup.conf'''
}
}
stage('Compile') {
steps {
sh '''#!/usr/bin/env bash
set -o pipefail
rm -rf .sconf_temp .sconsign.dblite build-release
scons | tee compilation.txt'''
}
post {
failure {
uploadArtifact('compilation.txt', 'Compilation')
}
}
}
stage('Run tests') {
steps {
sh 'PYTHONPATH=$PWD/build-release/python/ python3 -m pytest --durations=0 --junitxml=results.xml build-release/tests'
}
}
}
post {
always {
createArtifact("results.xml")
junit 'results.xml'
step([$class: 'XUnitBuilder',
thresholds: [
[$class: 'SkippedThreshold', failureThreshold: '0'],
[$class: 'FailedThreshold', failureThreshold: '0']],
tools: [[$class: 'GoogleTestType', pattern: 'build-release/tests/gtest_results.xml']]])
}
success {
trigger_rtd()
passed_hbm()
}
failure {
failed_hbm()
emailext(
body: '''${SCRIPT, template="groovy-html.template"}''',
mimeType: 'text/html',
subject: "[Jenkins] ${currentBuild.fullDisplayName} Failed",
recipientProviders: [[$class: 'CulpritsRecipientProvider']],
to: 'lucas.frerot@protonmail.com',
attachLog: true,
compressLog: true)
}
}
}
def createArtifact(filename) {
sh "./tests/ci/scripts/hbm send-uri -k 'Jenkins URI' -u ${BUILD_URL} -l 'View Jenkins result'"
sh "./tests/ci/scripts/hbm send-junit-results -f ${filename}"
}
def uploadArtifact(artifact, name) {
sh "./test/ci/scripts/hbm upload-file -f ${artifact} -n \"${name}\" -v ${PROJECT_ID}"
}
def failed_hbm() {
sh "./tests/ci/scripts/hbm failed"
}
def passed_hbm() {
sh "./tests/ci/scripts/hbm passed"
}
def trigger_rtd() {
sh """
set -x
curl -X POST -d "token=${RTD_TOKEN}" https://readthedocs.org/api/v2/webhook/tamaas/106141/
"""
}
diff --git a/SConstruct b/SConstruct
index 4c109182..b83e4ff4 100644
--- a/SConstruct
+++ b/SConstruct
@@ -1,475 +1,478 @@
# -*- mode:python; coding: utf-8 -*-
# vim: set ft=python:
# @file
# LICENSE
#
# Copyright (©) 2016-2021 EPFL (École Polytechnique Fédérale de Lausanne),
# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as published
# by the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Affero General Public License for more details.
#
# You should have received a copy of the GNU Affero General Public License
# along with this program. If not, see <https://www.gnu.org/licenses/>.
# ------------------------------------------------------------------------------
# Imports
# ------------------------------------------------------------------------------
from __future__ import print_function
import sys
import os
from subprocess import check_output
# Import below not strictly necessary, but good for pep8
from SCons.Script import (
EnsurePythonVersion,
EnsureSConsVersion,
Help,
Environment,
Variables,
EnumVariable,
PathVariable,
BoolVariable,
ListVariable,
Split,
Export,
Dir,
)
from SCons.Errors import StopError
from SCons import __version__ as scons_version
from version import get_git_subst
from detect import (
FindFFTW,
FindBoost,
FindThrust,
FindCuda,
FindExpolit,
FindPybind11
)
from INFOS import TAMAAS_INFOS
# ------------------------------------------------------------------------------
EnsurePythonVersion(2, 7)
EnsureSConsVersion(2, 4)
# ------------------------------------------------------------------------------
def detect_dependencies(env):
"Detect all dependencies"
fftw_comp = {
'omp': ['omp'],
'threads': ['threads'],
'none': [],
}
fftw_components = fftw_comp[env['fftw_threads']]
if main_env['use_mpi']:
fftw_components.append('mpi')
FindFFTW(env, fftw_components, precision=env['real_type'])
FindBoost(env, ['boost/preprocessor/seq.hpp'])
FindExpolit(env)
thrust_var = 'THRUST_ROOT'
# Take cuda version of thrust if available
if 'CUDA_ROOT' in env['ENV']:
thrust_var = 'CUDA_ROOT'
FindThrust(env, env['backend'], thrust_var)
# Activate cuda if needed
if env['backend'] == 'cuda':
FindCuda(env)
if env['build_python']:
FindPybind11(env)
def subdir(env, dir):
"Building a sub-directory"
return env.SConscript(env.File('SConscript', dir),
variant_dir=env.Dir(dir, env['build_dir']),
duplicate=True)
# ------------------------------------------------------------------------------
# Main compilation
# ------------------------------------------------------------------------------
# Compilation colors
colors = {
'cyan': '\033[96m',
'purple': '\033[95m',
'blue': '\033[94m',
'green': '\033[92m',
'yellow': '\033[93m',
'gray': '\033[38;5;8m',
'orange': '\033[38;5;208m',
'red': '\033[91m',
'end': '\033[0m'
}
# Inherit all environment variables (for CXX detection, etc.)
main_env = Environment(
ENV=os.environ,
)
# Set tamaas information
for k, v in TAMAAS_INFOS.items():
main_env[k] = v
main_env['COLOR_DICT'] = colors
main_env.AddMethod(subdir, 'SubDirectory')
# Build variables
vars = Variables('build-setup.conf')
vars.AddVariables(
EnumVariable('build_type', 'Build type', 'release',
allowed_values=('release', 'profiling', 'debug'),
ignorecase=2),
EnumVariable('backend', 'Thrust backend', 'omp',
allowed_values=('cpp', 'omp', 'tbb'),
ignorecase=2),
EnumVariable('fftw_threads', 'Threads FFTW library preference', 'omp',
allowed_values=('omp', 'threads', 'none'),
ignorecase=2),
EnumVariable('sanitizer', 'Sanitizer type', 'none',
allowed_values=('none', 'memory', 'leaks', 'address'),
ignorecase=2),
PathVariable('prefix',
'Prefix where to install', '/usr/local'),
# Dependencies paths
PathVariable('FFTW_ROOT',
'FFTW custom path', os.getenv('FFTW_ROOT', ''),
PathVariable.PathAccept),
PathVariable('THRUST_ROOT',
'Thrust custom path', os.getenv('THRUST_ROOT', ''),
PathVariable.PathAccept),
PathVariable('BOOST_ROOT',
'Boost custom path', os.getenv('BOOST_ROOT', ''),
PathVariable.PathAccept),
PathVariable('CUDA_ROOT',
'Cuda custom path', os.getenv('CUDA_ROOT', ''),
PathVariable.PathAccept),
# Dependencies provided as submodule get different default
PathVariable('GTEST_ROOT',
'Googletest custom path',
os.getenv('GTEST_ROOT', '#third-party/googletest/googletest'),
PathVariable.PathAccept),
PathVariable('PYBIND11_ROOT',
'Pybind11 custom path',
os.getenv('PYBIND11_ROOT', '#third-party/pybind11/include'),
PathVariable.PathAccept),
PathVariable('EXPOLIT_ROOT',
'Expolit custom path',
os.getenv('EXPOLIT_ROOT', '#third-party/expolit/include'),
PathVariable.PathAccept),
# Executables
('CXX', 'Compiler', os.getenv('CXX', 'g++')),
('MPICXX', 'MPI Compiler wrapper', os.getenv('MPICXX', 'mpicxx')),
('py_exec', 'Python executable', 'python3'),
# Compiler flags
('CXXFLAGS', 'C++ compiler flags', os.getenv('CXXFLAGS', "")),
# Cosmetic
BoolVariable('verbose', 'Activate verbosity', False),
BoolVariable('color', 'Color the non-verbose compilation output', False),
# Tamaas components
BoolVariable('build_doc', 'Build documentation', False),
BoolVariable('build_tests', 'Build test suite', False),
BoolVariable('build_python', 'Build python wrapper', True),
# Documentation
ListVariable('doc_builders', 'Generated documentation formats',
default='html', names=Split("html man")), # TODO include latex
# Dependencies
BoolVariable('use_googletest', 'Build tests using GTest', False),
BoolVariable('use_mpi', 'Builds multi-process parallelism', False),
# Distribution options
BoolVariable('strip_info', 'Strip binary of added information', False),
BoolVariable('build_static_lib', "Build a static libTamaas", False),
# Type variables
EnumVariable('real_type', 'Type for real precision variables', 'double',
allowed_values=('double', 'long double')),
EnumVariable('integer_type', 'Type for integer variables', 'int',
allowed_values=('int', 'long')),
)
# Set variables of environment
vars.Update(main_env)
help_text = vars.GenerateHelpText(main_env)
help_text += """
Commands:
scons [build] [options]... Compile Tamaas (and additional modules/tests)
scons install [prefix=/your/prefix] [options]... Install Tamaas to prefix
scons dev Install symlink to Tamaas python module (useful to development purposes)
scons test Run tests with pytest
scons doc Compile documentation with Doxygen and Sphinx+Breathe
scons archive Create a gzipped archive from source
""" # noqa
Help(help_text)
# Save all options, not just those that differ from default
with open('build-setup.conf', 'w') as setup:
for option in vars.options:
setup.write("# " + option.help.replace('\n', '\n# ') + "\n")
setup.write("{} = '{}'\n".format(option.key, main_env[option.key]))
main_env['should_configure'] = \
not main_env.GetOption('clean') and not main_env.GetOption('help')
build_type = main_env['build_type']
build_dir = 'build-${build_type}'
main_env['build_dir'] = main_env.Dir(build_dir)
# Setting up the python name with version
if main_env['build_python']:
args = (main_env.subst("${py_exec} -c").split()
+ ["from distutils.sysconfig import get_python_version;"
"print(get_python_version())"])
main_env['py_version'] = bytes(check_output(args)).decode()
# Printing some build infos
if main_env['should_configure']:
print('-- SCons {} (Python {}.{})'.format(scons_version,
sys.version_info.major,
sys.version_info.minor))
print(main_env.subst("-- Build type: ${build_type}\n"
"-- Thrust backend: ${backend}\n"
"-- FFTW threads: ${fftw_threads}\n"
"-- MPI: ${use_mpi}\n"
"-- Build directory: ${build_dir}\n"
"-- Python version (bindings): $py_version"))
verbose = main_env['verbose']
# Remove colors if not set
if not main_env['color']:
for key in colors:
colors[key] = ''
if not verbose:
main_env['CXXCOMSTR'] = main_env['SHCXXCOMSTR'] = \
u'{0}[Compiling ($SHCXX)] {1}$SOURCE'.format(colors['green'],
colors['end'])
main_env['LINKCOMSTR'] = main_env['SHLINKCOMSTR'] = \
u'{0}[Linking] {1}$TARGET'.format(colors['purple'],
colors['end'])
main_env['ARCOMSTR'] = u'{}[Ar]{} $TARGET'.format(colors['purple'],
colors['end'])
main_env['RANLIBCOMSTR'] = \
u'{}[Randlib]{} $TARGET'.format(colors['purple'],
colors['end'])
main_env['PRINT_CMD_LINE_FUNC'] = pretty_cmd_print
+ main_env['INSTALLSTR'] = \
+ u'{}[Installing] {}$SOURCE to $TARGET'.format(colors['blue'],
+ colors['end'])
# Include paths
main_env.AppendUnique(CPPPATH=['#/src',
'#/src/core',
'#/src/mpi',
'#/src/bem',
'#/src/surface',
'#/src/python',
'#/src/percolation',
'#/src/model',
'#/src/model/elasto_plastic',
'#/src/solvers',
'#/src/gpu',
'#/python'])
# Changing the shared object extension
main_env['SHOBJSUFFIX'] = '.o'
# Back to gcc if cuda is activated
if main_env['backend'] == "cuda" and "g++" not in main_env['CXX']:
raise StopError('GCC should be used when compiling with CUDA')
# OpenMP flags - compiler dependent
omp_flags = {
"g++": ["-fopenmp"],
"clang++": ["-fopenmp"],
"icpc": ["-qopenmp"]
}
def cxx_alias(cxx):
for k in omp_flags.keys():
if k in cxx:
return k
raise StopError('Unsupported compiler: ' + cxx)
cxx = cxx_alias(main_env['CXX'])
# Setting main compilation flags
main_env['CXXFLAGS'] = Split(main_env['CXXFLAGS'])
main_env['LINKFLAGS'] = main_env['CXXFLAGS']
main_env.AppendUnique(
CXXFLAGS=Split('-std=c++14 -Wall -Wextra -pedantic'),
CPPDEFINES={
'TAMAAS_LOOP_BACKEND': 'TAMAAS_LOOP_BACKEND_${backend.upper()}',
'TAMAAS_FFTW_BACKEND': 'TAMAAS_FFTW_BACKEND_${fftw_threads.upper()}'
},
)
# Adding OpenMP flags
if main_env['backend'] == 'omp':
main_env.AppendUnique(CXXFLAGS=omp_flags[cxx])
main_env.AppendUnique(LINKFLAGS=omp_flags[cxx])
else:
main_env.AppendUnique(CXXFLAGS=['-Wno-unknown-pragmas'])
# Correct bug in clang?
if main_env['backend'] == 'omp' and cxx == "clang++":
main_env.AppendUnique(LIBS=["atomic"])
elif main_env['backend'] == 'tbb':
main_env.AppendUnique(LIBS=['tbb'])
# Manage MPI compiler
if main_env['use_mpi']:
main_env['CXX'] = '$MPICXX'
main_env.AppendUnique(CPPDEFINES=['TAMAAS_USE_MPI'])
main_env.AppendUnique(CXXFLAGS=['-Wno-cast-function-type'])
# Flags and options
if main_env['build_type'] == 'debug':
main_env.AppendUnique(CPPDEFINES=['TAMAAS_DEBUG'])
# Define the scalar types
main_env.AppendUnique(CPPDEFINES={'TAMAAS_REAL_TYPE': '${real_type}',
'TAMAAS_INT_TYPE': '${integer_type}'})
# Compilation flags
cxxflags_dict = {
"debug": Split("-g -O0"),
"profiling": Split("-g -O3 -fno-omit-frame-pointer"),
"release": Split("-O3")
}
if main_env['sanitizer'] != 'none':
if main_env['backend'] == 'cuda':
raise StopError(
"Sanitizers with cuda are not yet supported!")
cxxflags_dict[build_type].append('-fsanitize=${sanitizer}')
main_env.AppendUnique(CXXFLAGS=cxxflags_dict[build_type])
main_env.AppendUnique(SHLINKFLAGS=cxxflags_dict[build_type])
main_env.AppendUnique(LINKFLAGS=cxxflags_dict[build_type])
if main_env['should_configure']:
basic_checks(main_env)
detect_dependencies(main_env)
# Writing information file
main_env.Tool('textfile')
main_env['SUBST_DICT'] = get_git_subst()
# Empty values if requested
if main_env['strip_info']:
for k in main_env['SUBST_DICT']:
main_env['SUBST_DICT'][k] = ""
# Substitution of environment file
main_env['SUBST_DICT'].update({
'@build_type@': '$build_type',
'@build_dir@': '${build_dir.abspath}',
'@build_version@': '$version',
'@backend@': '$backend',
})
# Environment file content
env_content = """export PYTHONPATH=@build_dir@/python:$$PYTHONPATH
export LD_LIBRARY_PATH=@build_dir@/src:$$LD_LIBRARY_PATH
"""
# Writing environment file
env_file = main_env.Textfile(
main_env.File('tamaas_environment.sh', main_env['build_dir']),
env_content)
# Default targets
build_targets = ['build-cpp', env_file]
install_targets = ['install-lib']
if main_env._get_major_minor_revision(scons_version)[0] >= 4:
main_env.Tool('compilation_db')
main_env.CompilationDatabase(PRINT_CMD_LINE_FUNC=pretty_cmd_print)
# Building Tamaas library
Export('main_env')
main_env.SubDirectory('src')
# Building Tamaas extra components
for dir in ['python', 'tests']:
if main_env['build_{}'.format(dir)] and not main_env.GetOption('help'):
main_env.SubDirectory(dir)
build_targets.append('build-{}'.format(dir))
# Building API + Sphinx documentation if requested
if main_env['build_doc']:
main_env.SubDirectory('doc')
main_env.Alias('doc', 'build-doc')
install_targets.append('install-doc')
else:
dummy_command(main_env, 'doc', 'Command "doc" does not do anything'
' without documentation activated ("build_doc=True")')
# Define dummy dev command when python is deactivated
if not main_env['build_python']:
dummy_command(main_env, 'dev', 'Command "dev" does not do anything'
+ ' without python activated ("build_python=True")')
else:
install_targets.append('install-python')
# Define dummy test command when tests are deactivated
if not main_env['build_tests']:
dummy_command(main_env, 'test', 'Command "test" does not do anything'
+ ' without tests activated ("build_tests=True")')
# Definition of target aliases, a.k.a. sub-commands
main_env.Alias('build', build_targets)
# Define proper install targets
main_env.Alias('install', install_targets)
# Default target is to build stuff
main_env.Default('build')
# Building a tar archive
archive = main_env.Command(
'tamaas-${version}.tar.gz',
'',
('tar --exclude-vcs --exclude-vcs-ignores '
'--exclude=third-party/googletest '
'--exclude=third-party/pybind11 '
'--exclude=joss '
'--exclude=".*" '
'-czf $TARGET {}'.format(Dir('.').name)),
chdir='..',
)
main_env.Alias('archive', archive)
diff --git a/python/SConscript b/python/SConscript
index d31d2948..6d0da3bd 100644
--- a/python/SConscript
+++ b/python/SConscript
@@ -1,160 +1,163 @@
# -*- mode:python; coding: utf-8 -*-
# vim: set ft=python:
# @file
# LICENSE
#
# Copyright (©) 2016-2021 EPFL (École Polytechnique Fédérale de Lausanne),
# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as published
# by the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Affero General Public License for more details.
#
# You should have received a copy of the GNU Affero General Public License
# along with this program. If not, see <https://www.gnu.org/licenses/>.
from __future__ import print_function
from SCons.Script import Import, Split, Copy, Dir
Import('main_env')
# Pybind11 wrapper
env_pybind = main_env.Clone(SHLIBPREFIX='')
# Remove pedantic warnings
cxx_flags = env_pybind['CXXFLAGS']
try:
del cxx_flags[cxx_flags.index('-pedantic')]
except ValueError:
pass
env_pybind.Tool(pybind11)
pybind_sources = Split("""
tamaas_module.cpp
wrap/core.cpp
wrap/percolation.cpp
wrap/surface.cpp
wrap/model.cpp
wrap/solvers.cpp
wrap/compute.cpp
wrap/mpi.cpp
wrap/test_features.cpp
""")
# Setting paths to find libTamaas
env_pybind.AppendUnique(LIBPATH=['../src'])
# Link against a static libTamaas
if env_pybind['build_static_lib']:
env_pybind.PrependUnique(LIBS=['Tamaas']) # keep other libs for link
env_pybind['RPATH'] = "" # no need for rpath w/ static lib
# Link against a dynamic libTamaas
else:
env_pybind.AppendUnique(RPATH=[
"'$$$$ORIGIN/../../src'", # path to lib in build_dir
"'$$$$ORIGIN/../../..'", # path to lib in install prefix
])
env_pybind['LIBS'] = ['Tamaas'] # discard other libs for link
# Building the pybind library
tamaas_wrap = env_pybind.Pybind11Module(
target='tamaas/_tamaas',
source=pybind_sources,
)
# For some reason link happens too early
Import('libTamaas')
env_pybind.Depends(tamaas_wrap, libTamaas)
# Copying the __init__.py file with extra python classes
copy_env = env_pybind.Clone()
# Copying additional python files
python_files = """
__main__.py
compute.py
dumpers/__init__.py
dumpers/_helper.py
nonlinear_solvers/__init__.py
""".split()
targets = [tamaas_wrap]
targets += [
copy_env.Command(copy_env.File(f, 'tamaas'),
copy_env.File(f, '#python/tamaas'),
Copy("$TARGET", "$SOURCE"))
for f in python_files
]
targets.append(copy_env.Command('MANIFEST.in', '#python/MANIFEST.in',
Copy("$TARGET", "$SOURCE")))
subst_env = env_pybind.Clone(
SUBST_DICT={
'@version@': '$version',
'@authors@': str(copy_env['authors']),
'@email@': '$email',
# TODO change when issue with unicode fixed
# '@copyright@': '$copyright',
# '@maintainer@': '$maintainer',
}
)
subst_env.Tool('textfile')
targets.append(subst_env.Substfile('setup.py.in'))
targets.append(subst_env.Substfile('tamaas/__init__.py.in'))
# Defining alias for python builds
main_env.Alias('build-python', targets)
# Checking if we can use pip to install (more convenient for end-user)
install_env = main_env.Clone()
conf = Configure(install_env,
custom_tests={'CheckPythonModule': CheckPythonModule})
has_pip = conf.CheckPythonModule('pip')
install_env = conf.Finish()
# Current build directory
install_env['PYDIR'] = Dir('.')
# Setting command line for installation
if has_pip:
install_env['PYINSTALLCOM'] = '${py_exec} -m pip install -U $PYOPTIONS .'
install_env['PYDEVELOPCOM'] = \
'${py_exec} -m pip install $PYOPTIONS -e .[all]'
else:
install_env['PYINSTALLCOM'] = '${py_exec} setup.py install $PYOPTIONS'
install_env['PYDEVELOPCOM'] = '${py_exec} setup.py develop $PYOPTIONS'
install_env['py_version'] = get_python_version(install_env)
install_env.PrependENVPath(
'PYTHONPATH',
install_env.subst('${prefix}/lib/python${py_version}/site-packages'))
# Specify install target
+PYOPTIONS = ['${"" if verbose else "-q"}']
python_install = install_env.Command(
'.python_install_phony',
- targets, install_env['PYINSTALLCOM'], PYOPTIONS='--prefix ${prefix}',
+ targets, install_env['PYINSTALLCOM'],
+ PYOPTIONS=['--prefix', '${prefix}'] + PYOPTIONS,
chdir=install_env['PYDIR'])
python_install_dev = install_env.Command(
'.python_install_local_phony',
- targets, install_env['PYDEVELOPCOM'], PYOPTIONS='--user',
+ targets, install_env['PYDEVELOPCOM'],
+ PYOPTIONS=['--user'] + PYOPTIONS,
chdir=install_env['PYDIR'])
# Defining aliases
main_env.Alias('install-python', python_install)
main_env.Alias('dev', python_install_dev)
diff --git a/site_scons/site_init.py b/site_scons/site_init.py
index 39205752..99b39e1c 100644
--- a/site_scons/site_init.py
+++ b/site_scons/site_init.py
@@ -1,179 +1,191 @@
# -*- coding: utf-8 -*-
# @file
# LICENSE
#
# Copyright (©) 2016-2021 EPFL (École Polytechnique Fédérale de Lausanne),
# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as published
# by the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Affero General Public License for more details.
#
# You should have received a copy of the GNU Affero General Public License
# along with this program. If not, see <https://www.gnu.org/licenses/>.
import subprocess
from detect import FindPybind11
from SCons.Script import Configure
from SCons.Errors import StopError
# ------------------------------------------------------------------------------
def pybind11(env):
"""A tool to configure pybind11"""
def execute(command):
return [line for line in subprocess.check_output(
command, universal_newlines=True).split('\n')
if line != ""]
# Create a clone so we do not modify env
clone = env.Clone()
# Set variables for clone
FindPybind11(clone)
includes = clone['CPPPATH']
# Extension of shared library for python
try:
extension = execute(
env.subst('${py_exec}-config --extension-suffix').split())[0]
except subprocess.CalledProcessError:
extension = ".so"
def pybind11_builder(env, target, source, **kwargs):
"""Create a pybind11 module"""
clone = env.Clone()
clone.AppendUnique(CPPPATH=includes)
clone['SHLIBSUFFIX'] = extension
clone.AppendUnique(SHLINKFLAGS=['-fvisibility=hidden'])
return clone.SharedLibrary(target, source, **kwargs)
# Add pseudo-builder to master environment
env.AddMethod(pybind11_builder, 'Pybind11Module')
# ------------------------------------------------------------------------------
def pretty_cmd_print(command, target, source, env):
colors = env['COLOR_DICT']
if 'Copy' in command:
color = colors['gray']
action = 'Copying'
elif 'Creating' in command:
color = colors['yellow']
action = 'Generating'
elif 'database' in command:
color = colors['yellow']
action = 'Generating'
+ elif 'pytest' in command:
+ color = colors['green']
+ action = 'Running tests'
+ target[0] = target[0].dir
+ elif 'pip' in command:
+ color = colors['blue']
+ if 'user' in command:
+ action = 'Symlinking'
+ target[0] = target[0].dir
+ elif 'prefix' in command:
+ action = 'Installing'
+ target[0] = env.subst(target[0].dir.path + ' to ${prefix}')
else:
print(command)
return
print("{color}[{action}] {end}{target}".format(
color=color,
end=colors['end'],
target=target[0],
action=action
))
# ------------------------------------------------------------------------------
def CheckPythonModule(context, module):
"""Checks the existence of a python module"""
context.Message('Checking for Python module {}... '.format(module))
env = context.sconf.env
command = [env.subst('${py_exec}'), '-c', 'import {}'.format(module)]
context.Log('Executing external command: {}\n'.format(command))
try:
subprocess.check_output(command, stderr=subprocess.STDOUT)
result = True
except subprocess.CalledProcessError as e:
result = False
output = bytes(e.output)
context.Log(output.decode() + '\n')
context.Result(result)
return result
# ------------------------------------------------------------------------------
def CheckCompilerFlag(context, flag):
"Check compiler provides flag"
context.Message('Checking compiler flag {}... '.format(
context.sconf.env.subst(flag)))
test_file = """
int main() {
return 0;
}
"""
env = context.sconf.env.Clone(CXXFLAGS=[flag],
LINKFLAGS=[flag])
context.sconf.env = env
result = context.TryLink(test_file, '.cpp')
context.Result(result)
return result
# ------------------------------------------------------------------------------
def dummy_command(env, command, error_msg):
"""Creates a dummy scons command"""
def print_error(*args, **kwargs):
print(error_msg)
def print_cmd(*args, **kwargs):
pass
comm = env.Command('#.phony_{}'.format(command),
'', print_error, PRINT_CMD_LINE_FUNC=print_cmd)
env.Alias(command, comm)
# ------------------------------------------------------------------------------
def get_python_version(env):
versions_script = """
from __future__ import print_function
from sysconfig import get_python_version
print(get_python_version())"""
version = subprocess.check_output([env['py_exec'], "-c", versions_script],
universal_newlines=True).replace('\n',
'')
print(version)
return version
# ------------------------------------------------------------------------------
def basic_checks(env):
custom_tests = {
'CheckCompilerFlag': CheckCompilerFlag,
}
conf = Configure(env, custom_tests=custom_tests)
if not conf.CheckCXX():
StopError('Could not find working C++ compiler')
for flag in env['CXXFLAGS']:
if not conf.CheckCompilerFlag(flag):
StopError('Compiler does not support flag {}'.format(flag))
def check_type(cpp_type, stl_header):
if not conf.CheckType(cpp_type,
'#include <{}>'.format(stl_header),
'cpp'):
StopError('Standard type {} is not available'.format(cpp_type))
check_type('std::multiplies<void>', 'functional')
check_type('std::unique_ptr<void>', 'memory')
conf.Finish()
diff --git a/tests/SConscript b/tests/SConscript
index eeba2985..737f1efa 100644
--- a/tests/SConscript
+++ b/tests/SConscript
@@ -1,213 +1,215 @@
# -*- mode:python; coding: utf-8 -*-
# vim: set ft=python:
# @file
# LICENSE
#
# Copyright (©) 2016-2021 EPFL (École Polytechnique Fédérale de Lausanne),
# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as published
# by the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Affero General Public License for more details.
#
# You should have received a copy of the GNU Affero General Public License
# along with this program. If not, see <https://www.gnu.org/licenses/>.
from __future__ import print_function
from SCons.Script import Split, Copy, Dir, Import
from detect import FindGTest, FindPybind11
# ------------------------------------------------------------------------------
def copyComStr(env, main):
if 'SHCXXCOMSTR' in main:
env['CXXCOMSTR'] = main['SHCXXCOMSTR']
if 'SHLINKCOMSTR' in main:
env['LINKCOMSTR'] = main['SHLINKCOMSTR']
# ------------------------------------------------------------------------------
def make_python_tests(env):
"""Copy python tests to build directory"""
test_env = env.Clone()
test_files = Split("""
test_hertz.py
test_westergaard.py
test_patch_westergaard.py
test_patch_plasticity.py
test_surface.py
test_hertz_disp.py
test_hertz_kato.py
test_saturated_pressure.py
test_flood_fill.py
test_integral_operators.py
test_dumper.py
test_tangential.py
test_boussinesq_surface.py
test_voigt.py
test_memory.py
test_epic.py
fftfreq.py
conftest.py
pytest.ini
""")
if env['use_mpi']:
test_files += ['test_mpi_routines.py', 'mpi_routines.py']
src_dir = "#/tests"
targets = [
test_env.Command(file, test_env.File(file, src_dir),
Copy("$TARGET", "$SOURCE"))
for file in test_files
]
test_env = env.Clone(tools=[pybind11])
# Helper module for integral operators
test_env['SHLIBPREFIX'] = ''
test_env.PrependUnique(LIBS=['Tamaas'])
register = test_env.Pybind11Module(
target="register_integral_operators",
source=["register_integral_operators.cpp"])
Import('libTamaas')
test_env.Depends(register, libTamaas)
targets.append(register)
return targets
# ------------------------------------------------------------------------------
def compile_google_test(env, gtest_path):
gtest_obj = env.Object('gtest.o',
[env.File("src/gtest-all.cc", gtest_path)])
return env.StaticLibrary('gtest', gtest_obj)
# ------------------------------------------------------------------------------
def make_google_tests(env):
gtest_dir = Dir(env['GTEST_ROOT'])
gtest_env = env.Clone(CPPPATH=[gtest_dir],
CXXFLAGS=['-pthread', '-isystem',
env.Dir('include', gtest_dir).path])
FindGTest(gtest_env)
libgtest = None
# Hugly hack to detect if we need to compile gtest submodule
if env['GTEST_ROOT'] == '#third-party/googletest/googletest':
gtest_path = str(gtest_dir)
libgtest = compile_google_test(gtest_env, gtest_path)
env.AppendUnique(CXXFLAGS=gtest_env['CXXFLAGS'])
env.PrependUnique(LIBS=['Tamaas', env.subst('python${py_version}')])
google_test_files = Split("""
test_fft.cpp
test_grid.cpp
test_loop.cpp
test_model.cpp
test_static_types.cpp
test_integration.cpp
""")
# Necessary for the tests that use pybind11 calls to python
uses = []
if env['build_python']:
google_test_files.append('test_fftfreq.cpp')
uses = ['TAMAAS_USE_PYTHON']
if env['use_mpi']:
google_test_files.append('test_mpi.cpp')
defines = env['CPPDEFINES']
if type(defines) is not list:
defines = [defines]
gtest_main = env.Object("tamaas_gtest_main.o", 'tamaas_gtest_main.cc',
CPPDEFINES=defines + uses)
gtest_all = env.Program('test_gtest_all', google_test_files + [gtest_main],
LIBS=(env['LIBS'] + ['gtest']))
Import('libTamaas')
env.Depends(gtest_all, libTamaas)
env.Depends(gtest_all, libgtest)
return [gtest_all]
# ------------------------------------------------------------------------------
def make_bare_tests(env):
rough = env.Program("test_rough_surface.cpp")
Import('libTamaas')
env.Depends(rough, libTamaas)
return [rough]
# ------------------------------------------------------------------------------
Import('main_env')
# Setup of test environment
test_env = main_env.Clone()
test_env.AppendUnique(
LIBPATH=['.', '../src'],
RPATH=["'$$$$ORIGIN/../src'"]
)
test_env.PrependUnique(LIBS=['Tamaas'])
# Building tests that do not require any third party
targets = make_bare_tests(test_env)
# Build tests that required python bindings
if test_env['build_python']:
FindPybind11(test_env)
test_env.Tool(pybind11)
test_env.ParseConfig("${py_exec}-config --ldflags")
test_env['CCFLAGS'] = []
targets += make_python_tests(test_env)
# Building google tests
if test_env['use_googletest']:
targets += make_google_tests(test_env)
targets.append(test_env.Command('test_gtest.py', '#tests/test_gtest.py',
Copy('$TARGET', '$SOURCE')))
# Target alias to build tests
main_env.Alias('build-tests', targets)
# Check if pytest is installed
conf = Configure(test_env,
custom_tests={'CheckPythonModule': CheckPythonModule})
has_pytest = conf.CheckPythonModule('pytest')
conf.Finish()
# Define a command to execute tests
if has_pytest:
pytest_env = test_env.Clone()
test_env['pythonpath'] = '${build_dir}/python'
test_env['ld_library_path'] = '${build_dir}/src'
pytest_env.PrependENVPath('PYTHONPATH', '${pythonpath.abspath}')
pytest_env.PrependENVPath('LD_LIBRARY_PATH', '${ld_library_path.abspath}')
# Setting a moderate thread number
pytest_env['ENV']['OMP_NUM_THREADS'] = "1"
- test_target = pytest_env.Command('.phony_test', targets,
- '${py_exec} -m pytest ${build_dir}/tests')
+ pytest_env['PYTESTOPTS'] = ['${"-v" if verbose else "-q"}']
+ test_target = pytest_env.Command(
+ '.phony_test', targets,
+ '${py_exec} -m pytest $PYTESTOPTS ${TARGET.dir}')
main_env.Alias('test', test_target)
else:
# We still define a target here so that `scons test` still works
dummy_command(main_env, 'test',
'Cannot run tests: pytest is not installed')
diff --git a/tests/conftest.py b/tests/conftest.py
index f1fb9f78..1c9337d8 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -1,309 +1,302 @@
# -*- coding: utf-8 -*-
# @file
# LICENSE
#
# Copyright (©) 2016-2021 EPFL (École Polytechnique Fédérale de Lausanne),
# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as published
# by the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Affero General Public License for more details.
#
# You should have received a copy of the GNU Affero General Public License
# along with this program. If not, see <https://www.gnu.org/licenses/>.
from __future__ import division, print_function
import subprocess
import sys
from functools import reduce
from operator import mul as multiply
import numpy as np
import pytest
from numpy.linalg import norm
try:
import tamaas as tm
except ModuleNotFoundError as e:
print(e, file=sys.stderr)
print("Use 'scons test' to run tests", file=sys.stderr)
sys.exit(1)
type_list = [tm.model_type.basic_1d,
tm.model_type.basic_2d,
tm.model_type.surface_1d,
tm.model_type.surface_2d,
tm.model_type.volume_1d,
tm.model_type.volume_2d]
def get_libtamaas_file():
try:
ldd_out = bytes(subprocess.check_output(['ldd', tm._tamaas.__file__]))
for line in filter(lambda x: 'Tamaas' in x,
ldd_out.decode().split('\n')):
path = line.split(' => ')[1]
return path.split(' ')[0]
return "static link"
except subprocess.CalledProcessError:
return "N/A"
def pytest_report_header(config):
print('tamaas build type: {}\nmodule file: {}\nwrapper: {}\nlibTamaas: {}'
.format(tm.TamaasInfo.build_type,
tm.__file__,
tm._tamaas.__file__,
get_libtamaas_file()))
def pytest_addoption(parser):
pass
# try:
# parser.addoption(
# '--with-mpi', action="store_true", default=False,
# help="Run MPI tests, this should be paired with mpirun."
# )
# except ValueError:
# pass
def mtidfn(val):
return str(val).split('.')[-1]
def pkridfn(val):
return {tm.PolonskyKeerRey.pressure: "pkr_pressure",
tm.PolonskyKeerRey.gap: "pkr_gap"}[val]
def profile(func, domain, N, modes, amplitude):
coords = [np.linspace(0, d, n, endpoint=False, dtype=tm.dtype)
for n, d in zip(N, domain)]
coords = np.meshgrid(*coords, indexing='ij')
sines = [func(2 * np.pi * x * m) for x, m in zip(coords, modes)]
return reduce(multiply, [amplitude] + sines)
-@pytest.fixture(scope="package", autouse=True)
-def tamaas_fixture():
- tm.initialize()
- yield None
- tm.finalize()
-
-
class HertzFixture:
def __init__(self, n, load):
self.domain_size = 1
self.n = n
self.load = load
self.curvature = 0.1
self.radius = 1. / self.curvature
self.e_star = 1.
self.a = (3 * load / (4 * self.curvature * self.e_star))**(1. / 3.)
self.x = np.linspace(-self.domain_size / 2.,
self.domain_size / 2.,
self.n, dtype=tm.dtype)
self.y = self.x.copy()
self.x, self.y = np.meshgrid(self.x, self.y)
self._computeSurface()
self._computePressure()
self._computeDisplacement()
def _computeDisplacement(self):
r = np.sqrt(self.x**2 + self.y**2)
self.displacement = np.zeros_like(r)
contact = r < self.a
self.displacement[contact] = self.surface[contact]
self.displacement[~contact] = \
(self.surface[~contact]
+ self.a / (np.pi * self.radius) * np.sqrt(r[~contact]**2
- self.a**2)
+ (r[~contact]**2 - 2 * self.a**2) / (np.pi * self.radius)
* np.arccos(self.a / r[~contact]))
def _computePressure(self):
r = np.sqrt(self.x**2 + self.y**2)
self.pressure = np.zeros_like(r)
contact = np.where(r < self.a)
self.pressure[contact] = \
2 * self.e_star / (np.pi * self.radius) \
* np.sqrt(self.a**2 - r[contact]**2)
def _computeSurface(self):
self.surface = -1. / (2 * self.radius) * (self.x**2 + self.y**2)
@pytest.fixture(scope="package")
def hertz():
return HertzFixture(1024, 0.00001)
@pytest.fixture(scope="package")
def hertz_coarse():
return HertzFixture(512, 0.0001)
@pytest.fixture(scope="package",
params=[tm.PolonskyKeerRey.pressure],
ids=pkridfn)
def pkr(hertz, request):
model = tm.ModelFactory.createModel(tm.model_type.basic_2d,
[hertz.domain_size, hertz.domain_size],
[hertz.n, hertz.n])
model.E, model.nu = hertz.e_star, 0
solver = tm.PolonskyKeerRey(model, hertz.surface, 1e-12,
request.param,
request.param)
solver.solve(hertz.load)
return model, hertz
class WestergaardFixture:
def __init__(self, n, load):
self.domain_size = 1.
self.lamda = 1.
self.delta = 0.1
self.e_star = 1.
self.n = n
self.p_star = np.pi * self.e_star * self.delta / self.lamda
self.load = load * self.p_star
self.a = self.lamda / np.pi \
* np.arcsin(np.sqrt(self.load / self.p_star))
self.x = np.linspace(-self.domain_size / 2.,
self.domain_size / 2.,
self.n, endpoint=False, dtype=tm.dtype)
self._computeSurface()
self._computePressure()
self._computeDisplacement()
def _computeSurface(self):
self.surface = self.delta * np.cos(2 * np.pi * self.x / self.lamda)
def _computePressure(self):
self.pressure = np.zeros_like(self.surface)
contact = np.where(np.abs(self.x) < self.a)
self.pressure[contact] = 2 * self.load \
* (np.cos(np.pi * self.x[contact] / self.lamda)
/ np.sin(np.pi * self.a / self.lamda)**2) \
* np.sqrt(np.sin(np.pi * self.a / self.lamda)**2 -
np.sin(np.pi * self.x[contact] / self.lamda)**2)
def _computeDisplacement(self):
psi = np.pi * np.abs(self.x) / self.lamda
psi_a = np.pi * self.a / self.lamda
with np.errstate(invalid='ignore'): # get some warnings out of the way
self.displacement = (np.cos(2*psi) + 2 * np.sin(psi)
* np.sqrt(np.sin(psi)**2 - np.sin(psi_a)**2)
- 2 * np.sin(psi_a)**2 *
np.log((np.sin(psi) +
np.sqrt(np.sin(psi)**2
- np.sin(psi_a)**2))
/ np.sin(psi_a)))
contact = np.where(np.abs(self.x) < self.a)
self.displacement[contact] = np.cos(2*psi[contact])
self.displacement *= self.load * self.lamda / (np.pi * self.e_star
* np.sin(psi_a)**2)
@pytest.fixture(scope="package")
def westergaard():
return WestergaardFixture(19683, 0.1)
class PatchWestergaard:
def __init__(self, model_type):
dim = tm.type_traits[model_type].dimension
bdim = tm.type_traits[model_type].boundary_dimension
domain = [1.] * dim
size = [6] * dim
self.modes = np.random.randint(1, 3, (bdim,))
self.model = tm.ModelFactory.createModel(model_type, domain, size)
self.model.E = 3.
self.model.nu = 0.
self.pressure = profile(np.cos, self.model.boundary_system_size,
self.model.boundary_shape, self.modes, 1)
self.solution = profile(
np.cos, self.model.boundary_system_size,
self.model.boundary_shape, self.modes,
1 / (np.pi * self.model.E_star * norm(self.modes)))
@pytest.fixture(scope="package",
params=set(type_list) - {tm.model_type.volume_1d},
ids=mtidfn)
def patch_westergaard(request):
return PatchWestergaard(request.param)
class UniformPlasticity:
def __init__(self, model_type, domain, sizes):
self.n = sizes
self.domain = domain
self.model = tm.ModelFactory.createModel(model_type, domain,
sizes)
self.E_h = 0.1
self.sigma_y = 0.01
self.residual = tm.ModelFactory.createResidual(self.model,
sigma_y=self.sigma_y,
hardening=self.E_h)
self.model.E = 1.
self.model.nu = 0.
def solution(self, p):
E, nu = self.model.E, self.model.nu
E_h, sigma_y = self.E_h, self.sigma_y
mu = E / (2 * (1 + nu))
strain = -1 / (mu + E_h) * (p * (3 * mu + E_h) / (2 * mu)
- np.sign(p) * sigma_y)
dep = (2 * mu * np.abs(strain) - sigma_y) / (3 * mu + E_h)
plastic_strain = np.sign(strain) / 2 * dep * np.array([
-1, -1, 2, 0, 0, 0,
], dtype=tm.dtype)
stress = 2 * mu * (np.array([
0, 0, strain, 0, 0, 0
], dtype=tm.dtype) - plastic_strain)
return {
"stress": stress,
"plastic_strain": plastic_strain,
"cumulated_plastic_strain": dep
}, {
"stress": mu,
"plastic_strain": 1,
"cumulated_plastic_strain": 1
}
@pytest.fixture(params=[tm.model_type.volume_2d],
ids=mtidfn)
def patch_isotropic_plasticity(request):
return UniformPlasticity(request.param, [1., 1., 1.], [4, 4, 4])