diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 2bf9b83..4c7ff9c 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -1,228 +1,228 @@ stages: - docker - lint - build - test - deploy variables: IMAGE_TAG: $CI_REGISTRY_IMAGE:$CI_COMMIT_REF_SLUG GIT_SUBMODULE_STRATEGY: recursive BUILD_DIR: build-release cache: key: "$CI_COMMIT_REF_SLUG" # ------------------------------------------------------------------------------ .docker_build: stage: docker image: docker:19.03.12 services: - docker:19.03.12-dind variables: # Use TLS https://docs.gitlab.com/ee/ci/docker/using_docker_build.html#tls-enabled DOCKER_HOST: tcp://docker:2376 DOCKER_TLS_CERTDIR: "/certs" DEFAULT_IMAGE: $CI_REGISTRY_IMAGE:$CI_DEFAULT_BRANCH before_script: - docker login -u $CI_REGISTRY_USER -p $CI_REGISTRY_PASSWORD $CI_REGISTRY script: - docker pull $DEFAULT_IMAGE-$IMAGE_NAME || true - docker build --cache-from $DEFAULT_IMAGE-$IMAGE_NAME -t $IMAGE_TAG-$IMAGE_NAME -f $DOCKERFILE . - docker push $IMAGE_TAG-$IMAGE_NAME docker build:debian: variables: IMAGE_NAME: debian-stable DOCKERFILE: tests/ci/docker/debian.mpi extends: .docker_build docker build:manylinux: variables: IMAGE_NAME: manylinux DOCKERFILE: tests/ci/docker/manylinux extends: .docker_build docker build:cuda: variables: IMAGE_NAME: cuda DOCKERFILE: tests/ci/docker/ubuntu_lts.cuda extends: .docker_build # ------------------------------------------------------------------------------ .debian_stable: variables: output: ${CI_COMMIT_REF_SLUG}-debian-stable image: ${IMAGE_TAG}-debian-stable .manylinux: variables: output: ${CI_COMMIT_REF_SLUG}-manylinux image: ${IMAGE_TAG}-manylinux .cuda: variables: output: ${CI_COMMIT_REF_SLUG}-cuda image: ${IMAGE_TAG}-cuda # ------------------------------------------------------------------------------ lint: stage: lint extends: - .debian_stable allow_failure: true script: - git remote remove upstream || true - git remote add upstream "$CI_PROJECT_URL" - git fetch upstream - '[ -z "$CI_MERGE_REQUEST_TARGET_BRANCH_NAME" ] && HEAD="$CI_COMMIT_BEFORE_SHA" || HEAD="upstream/$CI_MERGE_REQUEST_TARGET_BRANCH_NAME"' - echo "$HEAD" - - git-clang-format --diff "$HEAD" > clang_format.patch 2&>1 - - grep "no modified files to format" clang_format.patch + - git-clang-format --diff "$HEAD" > clang_format.patch 2>&1 + - grep "no modified files to format" clang_format.patch || grep "clang-format did not modify any files" clang_format.patch artifacts: when: on_failure paths: - clang_format.patch .build: stage: build variables: COMPILE_LOG: compilation.log script: - scons 2>&1 | tee $COMPILE_LOG artifacts: when: always paths: - build-setup.conf - $COMPILE_LOG - $BUILD_DIR - config.log .ccache: variables: CCACHE_BASEDIR: $CI_PROJECT_DIR/$BUILD_DIR CCACHE_DIR: $CI_PROJECT_DIR/.ccache CCACHE_NOHASDIR: 1 CCACHE_COMPILERCHECK: content CXX: /usr/lib/ccache/g++ OMPI_CXX: ${CXX} cache: key: ${output} policy: pull-push paths: - .ccache after_script: - ccache --show-stats || true build:mpi: extends: - .build - .debian_stable - .ccache before_script: - ccache --zero-stats || true - scons build_tests=True use_googletest=True build_python=True py_exec=python3 use_mpi=True backend=omp fftw_threads=omp verbose=True -h build:cuda: extends: - .build - .cuda before_script: - scons build_tests=True use_googletest=True build_python=True py_exec=python3 use_mpi=False backend=cuda fftw_threads=none verbose=True -h # ------------------------------------------------------------------------------ test:mpi: stage: test dependencies: - build:mpi extends: .debian_stable variables: PYTHONPATH: $CI_PROJECT_DIR/$BUILD_DIR/python TESTS: $BUILD_DIR/tests JUNITXML: results.xml TESTS_LOG: tests.log script: - ls $PYTHONPATH - python3 -c 'import sys; print(sys.path)' - python3 -m pytest -vvv --last-failed --durations=0 --junitxml=$JUNITXML $TESTS 2>&1 | tee $TESTS_LOG after_script: - python3 -m pytest --cache-show || true artifacts: when: always paths: - $JUNITXML - $TESTS_LOG reports: junit: - $JUNITXML cache: key: ${output}-pytest policy: pull-push paths: - .pytest_cache # ------------------------------------------------------------------------------ .protected_refs: extends: .manylinux rules: - if: '$CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH || $CI_COMMIT_TAG =~ /^v.*/' wheels: stage: build extends: - .protected_refs - .ccache before_script: - ccache --zero-stats || true script: - ./tests/ci/build_wheels.sh artifacts: paths: - dist/wheelhouse # ------------------------------------------------------------------------------ .deploy_wheels: stage: deploy extends: .protected_refs dependencies: - wheels script: python -m twine upload --verbose dist/wheelhouse/* package:gitlab: extends: .deploy_wheels variables: TWINE_USERNAME: gitlab-ci-token TWINE_PASSWORD: ${CI_JOB_TOKEN} TWINE_REPOSITORY_URL: ${CI_API_V4_URL}/projects/${CI_PROJECT_ID}/packages/pypi package:pypi: extends: .deploy_wheels variables: TWINE_USERNAME: __token__ TWINE_PASSWORD: ${PYPI_TOKEN} rules: - if: '$CI_COMMIT_TAG =~ /^v.*/' diff --git a/src/core/statistics.cpp b/src/core/statistics.cpp index 6e409f3..86c0018 100644 --- a/src/core/statistics.cpp +++ b/src/core/statistics.cpp @@ -1,210 +1,211 @@ /* * SPDX-License-Indentifier: AGPL-3.0-or-later * * 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 . * */ /* -------------------------------------------------------------------------- */ #include "statistics.hh" #include "fft_engine.hh" #include "loop.hh" #include "static_types.hh" /* -------------------------------------------------------------------------- */ namespace tamaas { template -Real Statistics::computeRMSHeights(Grid& surface) { return std::sqrt(surface.var()); +Real Statistics::computeRMSHeights(Grid& surface) { + return std::sqrt(surface.var()); } template Real Statistics::computeSpectralRMSSlope(Grid& surface) { const auto h_size = GridHermitian::hermitianDimensions(surface.sizes()); auto wavevectors = FFTEngine::template computeFrequencies(h_size); wavevectors *= 2 * M_PI; // need q for slopes const auto psd = computePowerSpectrum(surface); const Real rms_slope_mean = Loop::reduce( [] CUDA_LAMBDA(VectorProxy q, const Complex& psd_val) { // Checking if we're in the zone that does not have hermitian symmetry if (std::abs(q.back()) < 1e-15) return q.l2squared() * psd_val.real(); return 2 * q.l2squared() * psd_val.real(); }, range>(wavevectors), psd); return std::sqrt(rms_slope_mean); } /* -------------------------------------------------------------------------- */ template GridHermitian Statistics::computePowerSpectrum(Grid& surface) { const auto h_size = GridHermitian::hermitianDimensions(surface.sizes()); GridHermitian psd(h_size, surface.getNbComponents()); FFTEngine::makeEngine()->forward(surface, psd); Real factor = 1. / surface.getGlobalNbPoints(); // Squaring the fourier transform of surface and normalizing Loop::loop( [factor] CUDA_LAMBDA(Complex & c) { c *= factor; c *= conj(c); }, psd); return psd; } /* -------------------------------------------------------------------------- */ template Grid Statistics::computeAutocorrelation(Grid& surface) { Grid acf(surface.sizes(), surface.getNbComponents()); auto psd = computePowerSpectrum(surface); FFTEngine::makeEngine()->backward(acf, psd); acf *= acf.getGlobalNbPoints(); return acf; } /* -------------------------------------------------------------------------- */ template Real Statistics::contact(const Grid& tractions, UInt perimeter) { Real points = 0; UInt nc = tractions.getNbComponents(); switch (nc) { case 1: points = Loop::reduce( [] CUDA_LAMBDA(const Real& t) -> Real { return t > 0; }, tractions); break; case 2: points = Loop::reduce( [] CUDA_LAMBDA(VectorProxy t) -> Real { return t.back() > 0; }, range>(tractions)); break; case 3: points = Loop::reduce( [] CUDA_LAMBDA(VectorProxy t) -> Real { return t.back() > 0; }, range>(tractions)); break; default: TAMAAS_EXCEPTION("Invalid number of components in traction"); } auto area = points / tractions.getGlobalNbPoints(); if (dim == 1) perimeter = 0; // Correction from Yastrebov et al. (Trib. Intl., 2017) // 10.1016/j.triboint.2017.04.023 return area - (M_PI - 1 + std::log(2)) / (24. * tractions.getGlobalNbPoints()) * perimeter; } /* -------------------------------------------------------------------------- */ namespace { template class moment_helper { public: moment_helper(const std::array& exp) : exponent(exp) {} CUDA_LAMBDA Complex operator()(VectorProxy q, const Complex& phi) const { Real mul = 1; for (UInt i = 0; i < dim; ++i) mul *= std::pow(q(i), exponent[i]); // Do not duplicate everything from hermitian symmetry if (std::abs(q.back()) < 1e-15) return mul * phi; return 2 * mul * phi; } private: std::array exponent; }; } // namespace template <> std::vector Statistics<1>::computeMoments(Grid& surface) { constexpr UInt dim = 1; std::vector moments(3); const auto psd = computePowerSpectrum(surface); auto wavevectors = FFTEngine::template computeFrequencies(psd.sizes()); // we don't multiply by 2 pi because moments are computed with k moments[0] = Loop::reduce(moment_helper{{{0}}}, range(wavevectors), psd) .real(); moments[1] = Loop::reduce(moment_helper{{{2}}}, range(wavevectors), psd) .real(); moments[2] = Loop::reduce(moment_helper{{{4}}}, range(wavevectors), psd) .real(); return moments; } template <> std::vector Statistics<2>::computeMoments(Grid& surface) { constexpr UInt dim = 2; std::vector moments(3); const auto psd = computePowerSpectrum(surface); auto wavevectors = FFTEngine::template computeFrequencies(psd.sizes()); // we don't multiply by 2 pi because moments are computed with k moments[0] = Loop::reduce(moment_helper{{{0, 0}}}, range(wavevectors), psd) .real(); auto m02 = Loop::reduce(moment_helper{{{0, 2}}}, range(wavevectors), psd) .real(); auto m20 = Loop::reduce(moment_helper{{{2, 0}}}, range(wavevectors), psd) .real(); moments[1] = 0.5 * (m02 + m20); auto m22 = Loop::reduce(moment_helper{{{2, 2}}}, range(wavevectors), psd) .real(); auto m40 = Loop::reduce(moment_helper{{{4, 0}}}, range(wavevectors), psd) .real(); auto m04 = Loop::reduce(moment_helper{{{0, 4}}}, range(wavevectors), psd) .real(); moments[2] = (3 * m22 + m40 + m04) / 3.; return moments; } template struct Statistics<1>; template struct Statistics<2>; } // namespace tamaas