diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 2c6d464..52c7a83 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -2,9 +2,9 @@ name: build on: push: - branches: [ unstable, '[0-9]+.[0-9]+.x' ] + branches: [ notriqs, '[0-9]+.[0-9]+.x' ] pull_request: - branches: [ unstable, '[0-9]+.[0-9]+.x' ] + branches: [ notriqs, '[0-9]+.[0-9]+.x' ] workflow_call: workflow_dispatch: @@ -56,7 +56,6 @@ jobs: gfortran hdf5-tools libblas-dev - libboost-dev libclang-15-dev libc++-15-dev libc++abi-15-dev @@ -73,7 +72,6 @@ jobs: python3-clang-15 python3-dev python3-mako - python3-matplotlib python3-mpi4py python3-numpy python3-pip @@ -84,7 +82,7 @@ jobs: - name: Install homebrew dependencies if: matrix.os == 'macos-12' run: | - brew install ccache gcc@12 llvm boost fftw hdf5 open-mpi openblas + brew install ccache gcc@12 llvm hdf5 open-mpi openblas mkdir $HOME/.venv python3 -m venv $HOME/.venv/my_python source $HOME/.venv/my_python/bin/activate @@ -99,25 +97,13 @@ jobs: echo "PATH=/usr/local/opt/llvm/bin:$PATH" >> $GITHUB_ENV echo "CXXFLAGS=-stdlib=libc++" >> $GITHUB_ENV - - name: Build & Install TRIQS - env: - CC: ${{ matrix.cc }} - CXX: ${{ matrix.cxx }} - run: | - git clone https://github.com/TRIQS/triqs --branch ${{ github.ref_name }} - mkdir triqs/build && cd triqs/build - cmake .. -DBuild_Tests=OFF -DCMAKE_INSTALL_PREFIX=$HOME/install - make -j1 install VERBOSE=1 - cd ../ - - name: Build app4triqs env: CC: ${{ matrix.cc }} CXX: ${{ matrix.cxx }} LIBRARY_PATH: /usr/local/opt/llvm/lib run: | - source $HOME/install/share/triqs/triqsvars.sh - mkdir build && cd build && cmake .. + mkdir build && cd build && cmake .. -DCMAKE_INSTALL_PREFIX=$HOME/install make -j2 || make -j1 VERBOSE=1 - name: Test app4triqs @@ -125,7 +111,6 @@ jobs: DYLD_FALLBACK_LIBRARY_PATH: /usr/local/opt/llvm/lib OPENBLAS_NUM_THREADS: "1" run: | - source $HOME/install/share/triqs/triqsvars.sh cd build ctest -j2 --output-on-failure diff --git a/CMakeLists.txt b/CMakeLists.txt index 8033c5c..5616509 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -24,28 +24,22 @@ cmake_policy(VERSION ${CMAKE_VERSION}) # ############ # Define Project -project(app4triqs VERSION 3.3.0 LANGUAGES CXX) +project(app4triqs VERSION 1.3.0 LANGUAGES CXX) get_directory_property(IS_SUBPROJECT PARENT_DIRECTORY) -# ############ -# Load TRIQS and CPP2PY -find_package(TRIQS 3.3 REQUIRED) - -# Get the git hash & print status -triqs_get_git_hash_of_source_dir(PROJECT_GIT_HASH) +message(STATUS "-------- app4triqs version and git hash detection -------------") +find_package(Git) +execute_process(COMMAND ${GIT_EXECUTABLE} rev-parse HEAD + WORKING_DIRECTORY ${PROJECT_SOURCE_DIR} + OUTPUT_VARIABLE PROJECT_GIT_HASH + OUTPUT_STRIP_TRAILING_WHITESPACE +) message(STATUS "${PROJECT_NAME} version : ${PROJECT_VERSION}") message(STATUS "${PROJECT_NAME} Git hash: ${PROJECT_GIT_HASH}") -# Enforce Consistent Versioning -if(NOT ${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR} VERSION_EQUAL ${TRIQS_VERSION_MAJOR}.${TRIQS_VERSION_MINOR}) - message(FATAL_ERROR "The ${PROJECT_NAME} version ${PROJECT_VERSION} is not compatible with TRIQS version ${TRIQS_VERSION}.") -endif() - -# Default Install directory to TRIQS_ROOT if not given or when provided as relative path. +# Assert that install directory is provided and is absolute path. if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT OR (NOT IS_ABSOLUTE ${CMAKE_INSTALL_PREFIX})) - message(STATUS "No install prefix given (or invalid). Defaulting to TRIQS_ROOT") - set(CMAKE_INSTALL_PREFIX ${TRIQS_ROOT} CACHE PATH "default install path" FORCE) - set(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT FALSE) + message(FATAL_ERROR "No install prefix given (or invalid)") endif() if(NOT IS_SUBPROJECT) message(STATUS "-------- CMAKE_INSTALL_PREFIX: ${CMAKE_INSTALL_PREFIX} --------") @@ -68,9 +62,6 @@ endif() # Python Support option(PythonSupport "Build with Python support" ON) -if(PythonSupport AND NOT TRIQS_WITH_PYTHON_SUPPORT) - message(FATAL_ERROR "TRIQS was installed without Python support. Cannot build the Python Interface. Disable the build with -DPythonSupport=OFF") -endif() # Documentation option(Build_Documentation "Build documentation" OFF) @@ -122,6 +113,25 @@ target_compile_options(${PROJECT_NAME}_warnings $<$:-Wno-tautological-constant-compare> ) +# --------------------------------- +# Resolve Clang Linktime Problems +# CMake will adjust any linker flags from '-L path_to/mylib.so' to -lmylib +# if the proper mylib.so is automatically found by the linker, i.e. +# the directory comes first in LIBRARY_PATH. +# The clang linker however ignores LIBRARY_PATH. +# We thus explicitly add the content of LIBRARY_PATH to the LDFLAGS +# FIXME For future cmake versions we should populate the +# INTERFACE_LINK_DIRECTORIES of the triqs target +# --------------------------------- +if(CMAKE_CXX_COMPILER_ID MATCHES "Clang" AND DEFINED ENV{LIBRARY_PATH}) + string(REPLACE ":" ";" LINK_DIRS $ENV{LIBRARY_PATH}) + foreach(dir ${LINK_DIRS}) + string(APPEND CMAKE_SHARED_LINKER_FLAGS " -L${dir}") + string(APPEND CMAKE_MODULE_LINKER_FLAGS " -L${dir}") + string(APPEND CMAKE_EXE_LINKER_FLAGS " -L${dir}") + endforeach() +endif() + # Provide GNU Installation directories include(GNUInstallDirs) @@ -167,8 +177,7 @@ if(BUILD_DEBIAN_PACKAGE AND NOT IS_SUBPROJECT) set(CPACK_GENERATOR "DEB") set(CPACK_PACKAGE_VERSION ${PROJECT_VERSION}) set(CPACK_PACKAGE_CONTACT "https://github.com/TRIQS/${PROJECT_NAME}") - execute_process(COMMAND dpkg --print-architecture OUTPUT_VARIABLE CMAKE_DEBIAN_PACKAGE_ARCHITECTURE OUTPUT_STRIP_TRAILING_WHITESPACE) - set(CPACK_DEBIAN_PACKAGE_DEPENDS "triqs (>= 3.3)") + execute_process(COMMAND dpkg --print-architecture OUTPUT_VARIABLE CPACK_DEBIAN_PACKAGE_ARCHITECTURE OUTPUT_STRIP_TRAILING_WHITESPACE) set(CPACK_DEBIAN_PACKAGE_SHLIBDEPS ON) set(CPACK_DEBIAN_PACKAGE_GENERATE_SHLIBS ON) include(CPack) diff --git a/COPYING.txt b/COPYING.txt deleted file mode 100644 index 94a9ed0..0000000 --- a/COPYING.txt +++ /dev/null @@ -1,674 +0,0 @@ - GNU GENERAL PUBLIC LICENSE - Version 3, 29 June 2007 - - Copyright (C) 2007 Free Software Foundation, Inc. - Everyone is permitted to copy and distribute verbatim copies - of this license document, but changing it is not allowed. - - Preamble - - The GNU General Public License is a free, copyleft license for -software and other kinds of works. - - The licenses for most software and other practical works are designed -to take away your freedom to share and change the works. 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If your program is a subroutine library, you -may consider it more useful to permit linking proprietary applications with -the library. If this is what you want to do, use the GNU Lesser General -Public License instead of this License. But first, please read -. diff --git a/Dockerfile b/Dockerfile deleted file mode 100644 index 1ae1711..0000000 --- a/Dockerfile +++ /dev/null @@ -1,16 +0,0 @@ -# See ../triqs/packaging for other options -FROM flatironinstitute/triqs:unstable-ubuntu-clang -ARG APPNAME=app4triqs - -# Install here missing dependencies, e.g. -# RUN apt-get install -y python3-skimage - -COPY --chown=build . $SRC/$APPNAME -WORKDIR $BUILD/$APPNAME -RUN chown build . -USER build -ARG BUILD_ID -ARG CMAKE_ARGS -RUN cmake $SRC/$APPNAME -DTRIQS_ROOT=${INSTALL} $CMAKE_ARGS && make -j4 || make -j1 VERBOSE=1 -USER root -RUN make install diff --git a/Dockerfile.build b/Dockerfile.build new file mode 100644 index 0000000..0e403b4 --- /dev/null +++ b/Dockerfile.build @@ -0,0 +1,28 @@ +# See packaging for various base options +FROM flatironinstitute/triqs:base +ARG APPNAME=app4triqs + +# Install here missing dependencies, e.g. +# RUN apt-get install -y python3-skimage + +ARG BUILDUID=983 +RUN useradd -u $BUILDUID -m build + +ENV SRC=/src \ + BUILD=/home/build \ + INSTALL=/usr/local \ + PYTHONPATH=/usr/local/lib/python$PYTHON_VERSION/site-packages \ + CMAKE_PREFIX_PATH=/usr/lib/cmake/$APPNAME \ + OPENBLAS_NUM_THREADS=1 \ + MKL_NUM_THREADS=1 + +COPY --chown=build . $SRC/$APPNAME +WORKDIR $BUILD/$APPNAME +RUN chown build . +USER build +ARG BUILD_ID +ARG CMAKE_ARGS +ARG NCORES=4 +RUN cmake $SRC/$APPNAME -DCMAKE_INSTALL_PREFIX=$INSTALL -DCLANG_OPT="$CXXFLAGS" $CMAKE_ARGS && make -j$NCORES || make -j1 VERBOSE=1 +USER root +RUN make install diff --git a/Jenkinsfile b/Jenkinsfile index 00ed5be..2576c06 100644 --- a/Jenkinsfile +++ b/Jenkinsfile @@ -3,19 +3,16 @@ def projectName = "app4triqs" /* set to app/repo name */ def dockerName = projectName.toLowerCase(); /* which platform to build documentation on */ def documentationPlatform = "ubuntu-clang" -/* depend on triqs upstream branch/project */ -def triqsBranch = env.CHANGE_TARGET ?: env.BRANCH_NAME -def triqsProject = '/TRIQS/triqs/' + triqsBranch.replaceAll('/', '%2F') /* whether to keep and publish the results */ -def keepInstall = !env.BRANCH_NAME.startsWith("PR-") +def publish = !env.BRANCH_NAME.startsWith("PR-") properties([ disableConcurrentBuilds(), buildDiscarder(logRotator(numToKeepStr: '10', daysToKeepStr: '30')), - pipelineTriggers(keepInstall ? [ + pipelineTriggers(publish ? [ upstream( threshold: 'SUCCESS', - upstreamProjects: triqsProject + upstreamProjects: '/TRIQS/cpp2py/master,/TRIQS/h5/unstable' ) ] : []) ]) @@ -24,7 +21,7 @@ properties([ def platforms = [:] /****************** linux builds (in docker) */ -/* Each platform must have a corresponding Dockerfile.PLATFORM in triqs/packaging */ +/* Each platform must have a corresponding Dockerfile.PLATFORM in packaging */ def dockerPlatforms = ["ubuntu-clang", "ubuntu-gcc", "ubuntu-intel", "sanitize"] /* .each is currently broken in jenkins */ for (int i = 0; i < dockerPlatforms.size(); i++) { @@ -34,22 +31,22 @@ for (int i = 0; i < dockerPlatforms.size(); i++) { checkout scm /* construct a Dockerfile for this base */ sh """ - ( echo "FROM flatironinstitute/triqs:${triqsBranch}-${env.STAGE_NAME}" ; sed '0,/^FROM /d' Dockerfile ) > Dockerfile.jenkins - mv -f Dockerfile.jenkins Dockerfile + ( cat packaging/Dockerfile.${env.STAGE_NAME} ; sed '0,/^FROM /d' Dockerfile.build ) > Dockerfile """ /* build and tag */ def args = '' if (platform == documentationPlatform) - args = '-DBuild_Documentation=1' + args = '-DBuild_Documentation=1 -DMATHJAX_PATH=https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.2' else if (platform == "sanitize") args = '-DASAN=ON -DUBSAN=ON -DCMAKE_BUILD_TYPE=RelWithDebInfo' - def img = docker.build("flatironinstitute/${dockerName}:${env.BRANCH_NAME}-${env.STAGE_NAME}", "--build-arg APPNAME=${projectName} --build-arg BUILD_ID=${env.BUILD_TAG} --build-arg CMAKE_ARGS='${args}' .") + def uid = sh(returnStdout: true, script: "id -u").trim() + def img = docker.build("flatironinstitute/${dockerName}:${env.BRANCH_NAME}-${env.STAGE_NAME}", "--build-arg APPNAME=${projectName} --build-arg BUILD_ID=${env.BUILD_TAG} --build-arg CMAKE_ARGS='${args}' --build-arg BUILDUID=${uid} .") catchError(buildResult: 'UNSTABLE', stageResult: 'UNSTABLE') { img.inside("--shm-size=4gb") { sh "make -C \$BUILD/${projectName} test CTEST_OUTPUT_ON_FAILURE=1" } } - if (!keepInstall) { + if (!publish || platform != documentationPlatform) { sh "docker rmi --no-prune ${img.imageName()}" } } } } @@ -70,9 +67,8 @@ for (int i = 0; i < osxPlatforms.size(); i++) { def tmpDir = pwd(tmp:true) def buildDir = "$tmpDir/build" /* install real branches in a fixed predictable place so apps can find them */ - def installDir = keepInstall ? "${env.HOME}/install/${projectName}/${env.BRANCH_NAME}/${platform}" : "$tmpDir/install" - def triqsDir = "${env.HOME}/install/triqs/${triqsBranch}/${platform}" - def venv = triqsDir + def installDir = "$tmpDir/install" + def venv = installDir dir(installDir) { deleteDir() } @@ -92,9 +88,9 @@ for (int i = 0; i < osxPlatforms.size(); i++) { "VIRTUAL_ENV=$venv", "OMP_NUM_THREADS=2"]) { deleteDir() - /* note: this is installing into the parent (triqs) venv (install dir), which is thus shared among apps and so not be completely safe */ + sh "python3 -m venv $venv" sh "pip3 install -U -r $srcDir/requirements.txt" - sh "cmake $srcDir -DCMAKE_INSTALL_PREFIX=$installDir -DTRIQS_ROOT=$triqsDir" + sh "cmake $srcDir -DCMAKE_INSTALL_PREFIX=$installDir" sh "make -j2 || make -j1 VERBOSE=1" catchError(buildResult: 'UNSTABLE', stageResult: 'UNSTABLE') { try { sh "make test CTEST_OUTPUT_ON_FAILURE=1" @@ -112,7 +108,7 @@ for (int i = 0; i < osxPlatforms.size(); i++) { def error = null try { parallel platforms - if (keepInstall) { node('linux && docker && triqs') { + if (publish) { node('linux && docker && triqs') { /* Publish results */ stage("publish") { timeout(time: 5, unit: 'MINUTES') { def commit = sh(returnStdout: true, script: "git rev-parse HEAD").trim() diff --git a/LICENSE.txt b/LICENSE.txt index 4b35411..d645695 100644 --- a/LICENSE.txt +++ b/LICENSE.txt @@ -1,18 +1,202 @@ -app4triqs - An example application using triqs and cpp2py - -Copyright (C) 2017-2018, N. Wentzell, O. Parcollet -Copyright (C) 2018-2019, The Simons Foundation - authors: N. Wentzell, D. Simons, H. Strand, O. Parcollet - -app4triqs is free software: you can redistribute it and/or modify it under the -terms of the GNU General Public License as published by the Free Software -Foundation, either version 3 of the License, or (at your option) any later -version. - -app4triqs 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 General Public License for more details. - -You should have received a copy of the GNU General Public License along with -app4triqs (in the file COPYING.txt in this directory). If not, see -. + + Apache License + Version 2.0, January 2004 + http://www.apache.org/licenses/ + + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. 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We also recommend that a + file or class name and description of purpose be included on the + same "printed page" as the copyright notice for easier + identification within third-party archives. + + Copyright [yyyy] [name of copyright owner] + + Licensed under the Apache License, Version 2.0 (the "License"); + you may not use this file except in compliance with the License. + You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + + Unless required by applicable law or agreed to in writing, software + distributed under the License is distributed on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + See the License for the specific language governing permissions and + limitations under the License. diff --git a/README.md b/README.md index 1657290..a277b13 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,4 @@ -[![build](https://github.com/TRIQS/app4triqs/workflows/build/badge.svg)](https://github.com/TRIQS/app4triqs/actions?query=workflow%3Abuild) +[![build](https://github.com/TRIQS/app4triqs/workflows/build/badge.svg?branch=notriqs)](https://github.com/TRIQS/app4triqs/actions?query=workflow%3Abuild) # app4triqs - A skeleton for a TRIQS application diff --git a/c++/app4triqs/CMakeLists.txt b/c++/app4triqs/CMakeLists.txt index 5f51a38..9b78554 100644 --- a/c++/app4triqs/CMakeLists.txt +++ b/c++/app4triqs/CMakeLists.txt @@ -2,10 +2,11 @@ file(GLOB_RECURSE sources *.cpp) add_library(${PROJECT_NAME}_c ${sources}) add_library(${PROJECT_NAME}::${PROJECT_NAME}_c ALIAS ${PROJECT_NAME}_c) -# Link against triqs and enable warnings -target_link_libraries(${PROJECT_NAME}_c PUBLIC triqs PRIVATE $) +# Enable warnings +target_link_libraries(${PROJECT_NAME}_c PRIVATE $) # Configure target and compilation +target_compile_features(${PROJECT_NAME}_c PUBLIC cxx_std_23) set_target_properties(${PROJECT_NAME}_c PROPERTIES POSITION_INDEPENDENT_CODE ON VERSION ${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR} @@ -14,16 +15,17 @@ target_include_directories(${PROJECT_NAME}_c PUBLIC $) target_compile_definitions(${PROJECT_NAME}_c PUBLIC APP4TRIQS_GIT_HASH=${PROJECT_GIT_HASH} - TRIQS_GIT_HASH=${TRIQS_GIT_HASH} $<$:APP4TRIQS_DEBUG> - $<$:TRIQS_DEBUG> - $<$:TRIQS_ARRAYS_ENFORCE_BOUNDCHECK> ) # Install library and headers install(TARGETS ${PROJECT_NAME}_c EXPORT ${PROJECT_NAME}-targets DESTINATION ${CMAKE_INSTALL_LIBDIR}) install(DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} DESTINATION include FILES_MATCHING PATTERN "*.hpp" PATTERN "*.h") +# ========= Additional Depdencies ========== + +# Link against HDF5 C++ Interface +target_link_libraries(${PROJECT_NAME}_c PUBLIC h5::h5_c) # ========= Static Analyzer Checks ========== diff --git a/c++/app4triqs/app4triqs.hpp b/c++/app4triqs/app4triqs.hpp index d7ce7fc..5846e93 100644 --- a/c++/app4triqs/app4triqs.hpp +++ b/c++/app4triqs/app4triqs.hpp @@ -1,6 +1,4 @@ #pragma once -#include -#include #include
namespace app4triqs { diff --git a/deps/CMakeLists.txt b/deps/CMakeLists.txt index 392370c..930c3cf 100644 --- a/deps/CMakeLists.txt +++ b/deps/CMakeLists.txt @@ -65,3 +65,10 @@ external_dependency(GTest BUILD_ALWAYS EXCLUDE_FROM_ALL ) + +# -- h5 -- +external_dependency(h5 + GIT_REPO https://github.com/TRIQS/h5 + GIT_TAG unstable + BUILD_ALWAYS +) diff --git a/doc/CMakeLists.txt b/doc/CMakeLists.txt index 40eb49c..bc73e29 100644 --- a/doc/CMakeLists.txt +++ b/doc/CMakeLists.txt @@ -37,7 +37,6 @@ foreach(example ${ExampleList}) get_filename_component(d ${example} DIRECTORY) add_executable(${PROJECT_NAME}_doc_${f} EXCLUDE_FROM_ALL ${example}) set_property(TARGET ${PROJECT_NAME}_doc_${f} PROPERTY RUNTIME_OUTPUT_DIRECTORY ${d}) - target_link_libraries(${PROJECT_NAME}_doc_${f} triqs) add_custom_command(TARGET ${PROJECT_NAME}_doc_${f} COMMAND ${PROJECT_NAME}_doc_${f} > ${CMAKE_CURRENT_SOURCE_DIR}/${d}/${f}.output 2>/dev/null WORKING_DIRECTORY ${d} @@ -56,7 +55,7 @@ endif() add_custom_target(${PROJECT_NAME}_docs_sphinx ALL) add_custom_command( TARGET ${PROJECT_NAME}_docs_sphinx - COMMAND PYTHONPATH=${PROJECT_BINARY_DIR}/python:$ENV{PYTHONPATH} ${SPHINXBUILD_EXECUTABLE} -j auto -c . -b html ${CMAKE_CURRENT_SOURCE_DIR} html + COMMAND PYTHONPATH=${PROJECT_BINARY_DIR}/python:${h5_BINARY_DIR}/python:$ENV{PYTHONPATH} ${SPHINXBUILD_EXECUTABLE} -c . -j auto -b html ${CMAKE_CURRENT_SOURCE_DIR} html ) option(Sphinx_Only "When building the documentation, skip the Python Modules and the generation of C++ Api and example outputs" OFF) diff --git a/doc/_static/triqs_logo/Icon/JPG/Triqs_Icon_RGB_Black.jpg b/doc/_static/triqs_logo/Icon/JPG/Triqs_Icon_RGB_Black.jpg deleted file mode 100755 index a25819a..0000000 Binary files a/doc/_static/triqs_logo/Icon/JPG/Triqs_Icon_RGB_Black.jpg and /dev/null differ diff --git a/doc/_static/triqs_logo/Icon/JPG/Triqs_Icon_RGB_Full.jpg b/doc/_static/triqs_logo/Icon/JPG/Triqs_Icon_RGB_Full.jpg deleted file mode 100755 index 8fac42a..0000000 Binary files a/doc/_static/triqs_logo/Icon/JPG/Triqs_Icon_RGB_Full.jpg and /dev/null differ diff --git a/doc/_static/triqs_logo/Icon/SVG/Triqs_Icon_RGB_Black.svg b/doc/_static/triqs_logo/Icon/SVG/Triqs_Icon_RGB_Black.svg deleted file mode 100755 index ff59848..0000000 --- a/doc/_static/triqs_logo/Icon/SVG/Triqs_Icon_RGB_Black.svg +++ /dev/null @@ -1 +0,0 @@ - \ No newline at end of file diff --git a/doc/_static/triqs_logo/Icon/SVG/Triqs_Icon_RGB_Full.svg b/doc/_static/triqs_logo/Icon/SVG/Triqs_Icon_RGB_Full.svg deleted file mode 100755 index 76d6707..0000000 --- a/doc/_static/triqs_logo/Icon/SVG/Triqs_Icon_RGB_Full.svg +++ /dev/null @@ -1 +0,0 @@ - \ No newline at end of file diff --git a/doc/_static/triqs_logo/Icon/SVG/Triqs_Icon_RGB_White.svg b/doc/_static/triqs_logo/Icon/SVG/Triqs_Icon_RGB_White.svg deleted file mode 100755 index 4fbd963..0000000 --- a/doc/_static/triqs_logo/Icon/SVG/Triqs_Icon_RGB_White.svg +++ /dev/null @@ -1 +0,0 @@ - \ No newline at end of file diff --git a/doc/_static/triqs_logo/Logo/JPG/Triqs_Logo_RGB_Black.jpg b/doc/_static/triqs_logo/Logo/JPG/Triqs_Logo_RGB_Black.jpg deleted file mode 100755 index a9206e0..0000000 Binary files a/doc/_static/triqs_logo/Logo/JPG/Triqs_Logo_RGB_Black.jpg and /dev/null differ diff --git a/doc/_static/triqs_logo/Logo/JPG/Triqs_Logo_RGB_Full.jpg b/doc/_static/triqs_logo/Logo/JPG/Triqs_Logo_RGB_Full.jpg deleted file mode 100755 index 58e6a81..0000000 Binary files a/doc/_static/triqs_logo/Logo/JPG/Triqs_Logo_RGB_Full.jpg and /dev/null differ diff --git a/doc/_static/triqs_logo/Logo/SVG/Triqs_Logo_RGB_Black.svg b/doc/_static/triqs_logo/Logo/SVG/Triqs_Logo_RGB_Black.svg deleted file mode 100755 index 27ff0f4..0000000 --- a/doc/_static/triqs_logo/Logo/SVG/Triqs_Logo_RGB_Black.svg +++ /dev/null @@ -1 +0,0 @@ - \ No newline at end of file diff --git a/doc/_static/triqs_logo/Logo/SVG/Triqs_Logo_RGB_Full.svg b/doc/_static/triqs_logo/Logo/SVG/Triqs_Logo_RGB_Full.svg deleted file mode 100755 index 149bdb6..0000000 --- a/doc/_static/triqs_logo/Logo/SVG/Triqs_Logo_RGB_Full.svg +++ /dev/null @@ -1 +0,0 @@ - \ No newline at end of file diff --git a/doc/_static/triqs_logo/Logo/SVG/Triqs_Logo_RGB_White.svg b/doc/_static/triqs_logo/Logo/SVG/Triqs_Logo_RGB_White.svg deleted file mode 100755 index eb273f9..0000000 --- a/doc/_static/triqs_logo/Logo/SVG/Triqs_Logo_RGB_White.svg +++ /dev/null @@ -1 +0,0 @@ - \ No newline at end of file diff --git a/doc/_static/triqs_logo/triqs_favicon.ico b/doc/_static/triqs_logo/triqs_favicon.ico deleted file mode 100644 index 9e20d73..0000000 Binary files a/doc/_static/triqs_logo/triqs_favicon.ico and /dev/null differ diff --git a/doc/conf.py.in b/doc/conf.py.in index 3eb0de9..4737bfc 100644 --- a/doc/conf.py.in +++ b/doc/conf.py.in @@ -1,6 +1,6 @@ # -*- coding: utf-8 -*- # -# TRIQS documentation build configuration file +# documentation build configuration file import sys sys.path.insert(0, "@CMAKE_CURRENT_SOURCE_DIR@/sphinxext") @@ -65,9 +65,6 @@ html_theme = 'sphinx_rtd_theme' # this loads the custom css file to change the page width html_style = 'css/custom.css' -html_favicon = '@CMAKE_CURRENT_SOURCE_DIR@/_static/triqs_logo/triqs_favicon.ico' -#html_logo = '@CMAKE_CURRENT_SOURCE_DIR@/logos/logo.png' - # options for the the rtd theme html_theme_options = { 'logo_only': False, @@ -98,7 +95,7 @@ plot_include_source = True plot_html_show_source_link = False plot_html_show_formats = False -intersphinx_mapping = {'python': ('https://docs.python.org/3.11', None), 'triqslibs': ('https://triqs.github.io/triqs/latest', None)} +intersphinx_mapping = {'python': ('https://docs.python.org/3.11', None)} # open links in new tab instead of same window from sphinx.writers.html import HTMLTranslator diff --git a/doc/index.rst b/doc/index.rst index 94054b8..ddecd5e 100644 --- a/doc/index.rst +++ b/doc/index.rst @@ -14,7 +14,7 @@ app4triqs :target: https://github.com/triqs/app4triqs -An example application using cpp2py and :ref:`TRIQS `. +An example application using cpp2py. This documentation is generated based on `rst `_ files and the comments in the sources and headers. diff --git a/doc/install.rst b/doc/install.rst index 1c7766b..6674c16 100644 --- a/doc/install.rst +++ b/doc/install.rst @@ -8,13 +8,7 @@ Install app4triqs Compiling app4triqs from source =============================== -.. note:: To guarantee reproducibility in scientific calculations we strongly recommend the use of a stable `release `_ of both TRIQS and its applications. - -Prerequisites -------------- - -#. The :ref:`TRIQS ` library, see :ref:`TRIQS installation instruction `. - In the following, we assume that TRIQS is installed in the directory ``path_to_triqs``. +.. note:: To guarantee reproducibility in scientific calculations we strongly recommend the use of a stable `release `_ of app4triqs. Installation steps ------------------ @@ -27,13 +21,9 @@ Installation steps $ mkdir app4triqs.build && cd app4triqs.build -#. Ensure that your shell contains the TRIQS environment variables by sourcing the ``triqsvars.sh`` file from your TRIQS installation:: - - $ source path_to_triqs/share/triqs/triqsvars.sh - #. In the build directory call cmake, including any additional custom CMake options, see below:: - $ cmake ../app4triqs.src + $ cmake -DCMAKE_INSTALL_PREFIX=path_to_install_dir ../app4triqs.src #. Compile the code, run the tests and install the application:: @@ -41,12 +31,9 @@ Installation steps $ make test $ make install -Version compatibility ---------------------- +Versions +-------- -Keep in mind that the version of ``app4triqs`` must be compatible with your TRIQS library version, -see :ref:`TRIQS website `. -In particular the Major and Minor Version numbers have to be the same. To use a particular version, go into the directory with the sources, and look at all available versions:: $ cd app4triqs.src && git tag @@ -64,14 +51,14 @@ The compilation of ``app4triqs`` can be configured using CMake-options:: cmake ../app4triqs.src -DOPTION1=value1 -DOPTION2=value2 ... -+-----------------------------------------------------------------+-----------------------------------------------+ -| Options | Syntax | -+=================================================================+===============================================+ -| Specify an installation path other than path_to_triqs | -DCMAKE_INSTALL_PREFIX=path_to_app4triqs | -+-----------------------------------------------------------------+-----------------------------------------------+ -| Build in Debugging Mode | -DCMAKE_BUILD_TYPE=Debug | -+-----------------------------------------------------------------+-----------------------------------------------+ -| Disable testing (not recommended) | -DBuild_Tests=OFF | -+-----------------------------------------------------------------+-----------------------------------------------+ -| Build the documentation | -DBuild_Documentation=ON | -+-----------------------------------------------------------------+-----------------------------------------------+ ++-----------------------------------------+-----------------------------------------------+ +| Options | Syntax | ++=========================================+===============================================+ +| Specify an installation path | -DCMAKE_INSTALL_PREFIX=path_to_app4triqs | ++-----------------------------------------+-----------------------------------------------+ +| Build in Debugging Mode | -DCMAKE_BUILD_TYPE=Debug | ++-----------------------------------------+-----------------------------------------------+ +| Disable testing (not recommended) | -DBuild_Tests=OFF | ++-----------------------------------------+-----------------------------------------------+ +| Build the documentation | -DBuild_Documentation=ON | ++-----------------------------------------+-----------------------------------------------+ diff --git a/packaging/CMakeLists.txt b/packaging/CMakeLists.txt index 748dc4a..fbb0e42 100644 --- a/packaging/CMakeLists.txt +++ b/packaging/CMakeLists.txt @@ -2,6 +2,4 @@ configure_file(conda/meta.yaml.in conda/meta.yaml) configure_file(conda/build.sh conda/build.sh COPYONLY) configure_file(conda/conda_build_config.yaml conda/conda_build_config.yaml COPYONLY) -configure_file(TRIQS-app4triqs-foss-2021b.eb.in TRIQS-app4triqs-foss-2021b.eb) - - +configure_file(app4triqs-foss-2021b.eb.in app4triqs-foss-2021b.eb) diff --git a/packaging/Dockerfile.msan b/packaging/Dockerfile.msan new file mode 100644 index 0000000..bbfccb2 --- /dev/null +++ b/packaging/Dockerfile.msan @@ -0,0 +1,117 @@ +FROM --platform=linux/amd64 ubuntu:24.04 +ARG APPNAME=app4triqs +ARG LLVM=18 +ARG NTHREAD=10 + +RUN apt-get update && apt-get install -y lsb-release wget software-properties-common && \ + #wget -O /tmp/llvm.sh https://apt.llvm.org/llvm.sh && chmod +x /tmp/llvm.sh && /tmp/llvm.sh ${LLVM} && \ + DEBIAN_FRONTEND=noninteractive apt-get install -y \ + clang-${LLVM} \ + cmake \ + g++ \ + gfortran \ + git \ + vim \ + lldb-${LLVM} \ + hdf5-tools \ + libboost-dev \ + libclang-${LLVM}-dev \ + libomp-${LLVM}-dev \ + libfftw3-dev \ + libgfortran5 \ + libgmp-dev \ + libssl-dev \ + ninja-build \ + pkg-config \ + python3-clang-${LLVM} \ + python3-dev \ + python3-mako \ + python3-matplotlib \ + python3-numpy \ + python3-pip \ + python3-scipy + +ENV PYTHON_VERSION=3.12 \ + CC=clang-${LLVM} CXX=clang++-${LLVM} \ + LLVM_ROOT=/usr/lib/llvm-${LLVM} + +# Build libcxx and libcxxabi with MSAN +# c.f. https://github.com/google/sanitizers/wiki/MemorySanitizerLibcxxHowTo +RUN git clone https://github.com/llvm/llvm-project --branch release/${LLVM}.x --depth 1 -c advice.detachedHead=false /tmp/llvm_src && \ + mkdir /tmp/llvm_build && cd /tmp/llvm_build && \ + cmake /tmp/llvm_src/runtimes -G Ninja \ + -DLLVM_USE_SANITIZER=MemoryWithOrigins \ + -DCMAKE_BUILD_TYPE=RelWithDebInfo \ + -DCMAKE_INSTALL_PREFIX=${LLVM_ROOT} \ + -DLLVM_ENABLE_RUNTIMES="libcxx;libcxxabi" && \ + ninja -j${NTHREAD} install-cxx install-cxxabi + +# Build Environment using MSAN +# c.f. https://libcxx.llvm.org/UsingLibcxx.html#using-a-custom-built-libc +ENV MSAN_FLAGS="-fsanitize=memory -fno-omit-frame-pointer -fsanitize-recover=all -fsanitize-memory-track-origins -ggdb3" \ + CUSTOM_LIBCXX_FLAGS="-nostdinc++ -nostdlib++ -isystem${LLVM_ROOT}/include/c++/v1 -L${LLVM_ROOT}/lib -Wl,-rpath,${LLVM_ROOT}/lib -lc++ -lc++abi" +ENV CXXFLAGS="$MSAN_FLAGS -Wno-unused-command-line-argument $CUSTOM_LIBCXX_FLAGS" \ + CFLAGS="$MSAN_FLAGS" \ + MSAN_OPTIONS=symbolize=1:halt_on_error=1 \ + MSAN_SYMBOLIZER_PATH=${LLVM_ROOT}/bin/llvm-symbolizer + +# Static zlib using fPIC to be linked into hdf5 +ADD https://www.zlib.net/zlib-1.3.1.tar.gz /tmp/ +RUN cd /tmp && tar xf /tmp/zlib-1.3.1.tar.gz && cd zlib-1.3.1 && \ + CFLAGS="-fPIC $CFLAGS" ./configure --prefix=/opt/zlib && make -j${NTHREAD} && make install && \ + cd /tmp #&& rm -rf /tmp/zlib* + +# HDF5 +ADD https://github.com/HDFGroup/hdf5/archive/refs/tags/hdf5-1_14_3.tar.gz /tmp/ +RUN cd /tmp && tar xf /tmp/hdf5-1_14_3.tar.gz && chmod 1777 . && \ + mkdir build && cd build && \ + cmake /tmp/hdf5-hdf5-1_14_3 -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/opt/hdf5 \ + -DHDF5_ENABLE_Z_LIB_SUPPORT=ON -DZLIB_LIBRARY=/opt/zlib/lib/libz.a -DZLIB_INCLUDE_DIR:PATH=/opt/zlib/include && \ + make -j${NTHREAD} && make install && \ + cd /tmp && rm -rf /tmp/hdf5-* /tmp/build +ENV HDF5_ROOT=/opt/hdf5 + +# libevent +ADD https://github.com/libevent/libevent/releases/download/release-2.1.12-stable/libevent-2.1.12-stable.tar.gz /tmp/ +RUN cd /tmp && tar xf /tmp/libevent-2.1.12-stable.tar.gz && cd libevent-2.1.12-stable && \ + ./configure --prefix=/opt/openmpi --enable-shared && make -j${NTHREAD} && make install && \ + cd /tmp && rm -rf /tmp/libevent* + +# hwloc +ADD https://download.open-mpi.org/release/hwloc/v2.10/hwloc-2.10.0.tar.bz2 /tmp/ +COPY packaging/hwloc.patch /tmp/ +RUN cd /tmp && tar xf /tmp/hwloc-2.10.0.tar.bz2 && cd hwloc-2.10.0 && patch -p0 -i /tmp/hwloc.patch && \ + ./configure --prefix=/opt/openmpi --enable-shared && make -j${NTHREAD} && make install && \ + cd /tmp && rm -rf /tmp/hwloc* + +# OpenMPI +ADD https://download.open-mpi.org/release/open-mpi/v5.0/openmpi-5.0.2.tar.bz2 /tmp/ +RUN cd /tmp && tar xf /tmp/openmpi-5.0.2.tar.bz2 && cd openmpi-5.0.2 && \ + ./configure --prefix=/opt/openmpi --enable-shared --disable-mpi-fortran --disable-pty-support --with-hwloc=/opt/openmpi --with-libevent=/opt/openmpi && make -j${NTHREAD} && make install && \ + cd /tmp && rm -rf /tmp/openmpi-5.0.2* +ENV MPI_HOME=/opt/openmpi \ + MPICC=/opt/openmpi/bin/mpicc + +# Use libflame to provide blas / lapack +RUN git clone https://github.com/Wentzell/libflame /tmp/libflame && cd /tmp/libflame && \ + ./configure --prefix=/opt/libflame --enable-lapack2flame --enable-builtin-blas --build=x86_64-unknown-linux-gnu && make -j${NTHREAD} && make install && \ + cd /tmp && rm -rf /tmp/libflame + +RUN useradd -m build + +ENV SRC=/src \ + BUILD=/home/build \ + INSTALL=/usr/local \ + PYTHONPATH=/usr/local/lib/python${PYTHON_VERSION}/site-packages \ + CMAKE_PREFIX_PATH=/usr/lib/cmake/$APPNAME \ + OPENBLAS_NUM_THREADS=1 \ + MKL_NUM_THREADS=1 + +COPY . ${SRC}/$APPNAME +WORKDIR ${BUILD}/$APPNAME +RUN chown -R build . ${SRC}/$APPNAME +USER build +RUN cmake $SRC/$APPNAME -DCMAKE_INSTALL_PREFIX=$INSTALL -DCMAKE_BUILD_TYPE=Debug -DPythonSupport=OFF -DMSAN=ON \ + -DLAPACK_LIBRARIES="/opt/libflame/lib/libflame.a;gfortran" -DBLAS_LIBRARIES=/opt/libflame/lib/libflame.a && \ + make -j${NTHREAD} +RUN cd test/c++ && make test CTEST_OUTPUT_ON_FAILURE=1 || true diff --git a/packaging/Dockerfile.sanitize b/packaging/Dockerfile.sanitize new file mode 100644 index 0000000..89cf9b6 --- /dev/null +++ b/packaging/Dockerfile.sanitize @@ -0,0 +1,43 @@ +FROM ubuntu:24.04 +ARG LLVM=18 + +RUN apt-get update && apt-get install -y lsb-release wget software-properties-common && \ + #wget -O /tmp/llvm.sh https://apt.llvm.org/llvm.sh && chmod +x /tmp/llvm.sh && /tmp/llvm.sh ${LLVM} && \ + DEBIAN_FRONTEND=noninteractive apt-get install -y \ + clang-${LLVM} \ + cmake \ + g++ \ + gfortran \ + git \ + vim \ + lldb-${LLVM} \ + hdf5-tools \ + libboost-dev \ + libclang-${LLVM}-dev \ + libc++-${LLVM}-dev \ + libc++abi-${LLVM}-dev \ + libomp-${LLVM}-dev \ + libfftw3-dev \ + libgfortran5 \ + libgmp-dev \ + libhdf5-dev \ + libopenblas-dev \ + libopenmpi-dev \ + openmpi-bin \ + openmpi-common \ + openmpi-doc \ + python3-clang-${LLVM} \ + python3-dev \ + python3-mako \ + python3-matplotlib \ + python3-mpi4py \ + python3-numpy \ + python3-pip \ + python3-scipy + +ENV PYTHON_VERSION=3.12 \ + CC=clang-${LLVM} CXX=clang++-${LLVM} CXXFLAGS="-stdlib=libc++" \ + ASAN_SYMBOLIZER_PATH=/usr/lib/llvm-${LLVM}/bin/llvm-symbolizer \ + ASAN_OPTIONS=symbolize=1:detect_leaks=0:alloc_dealloc_mismatch=0 \ + UBSAN_OPTIONS=symbolize=1:print_stacktrace=1:halt_on_error=1 +RUN update-alternatives --install /usr/bin/clang clang /usr/bin/clang-${LLVM} 60 --slave /usr/bin/clang++ clang++ /usr/bin/clang++-${LLVM} --slave /usr/bin/clang-cpp clang-cpp /usr/bin/clang-cpp-${LLVM} diff --git a/packaging/Dockerfile.ubuntu-clang b/packaging/Dockerfile.ubuntu-clang new file mode 100644 index 0000000..f56868a --- /dev/null +++ b/packaging/Dockerfile.ubuntu-clang @@ -0,0 +1,49 @@ +FROM ubuntu:24.04 +ARG LLVM=18 + +# This platform includes dependencies for building docs +RUN apt-get update && apt-get install -y lsb-release wget software-properties-common && \ + #wget -O /tmp/llvm.sh https://apt.llvm.org/llvm.sh && chmod +x /tmp/llvm.sh && /tmp/llvm.sh ${LLVM} && \ + DEBIAN_FRONTEND=noninteractive apt-get install -y \ + clang-${LLVM} \ + cmake \ + g++ \ + gfortran \ + git \ + vim \ + lldb-${LLVM} \ + hdf5-tools \ + libboost-dev \ + libclang-${LLVM}-dev \ + libc++-${LLVM}-dev \ + libc++abi-${LLVM}-dev \ + libomp-${LLVM}-dev \ + libfftw3-dev \ + libgfortran5 \ + libgmp-dev \ + libhdf5-dev \ + libopenblas-dev \ + libopenmpi-dev \ + openmpi-bin \ + openmpi-common \ + openmpi-doc \ + pandoc \ + python3-clang-${LLVM} \ + python3-dev \ + python3-mako \ + python3-matplotlib \ + python3-mpi4py \ + python3-numpy \ + python3-numpydoc \ + python3-pip \ + python3-scipy \ + python3-ipython \ + python3-sphinx \ + python3-sphinx-rtd-theme \ + python3-nbsphinx \ + python3-myst-parser \ + python3-linkify-it + +ENV PYTHON_VERSION=3.12 \ + CC=clang-${LLVM} CXX=clang++-${LLVM} CXXFLAGS="-stdlib=libc++" +RUN update-alternatives --install /usr/bin/clang clang /usr/bin/clang-${LLVM} 60 --slave /usr/bin/clang++ clang++ /usr/bin/clang++-${LLVM} --slave /usr/bin/clang-cpp clang-cpp /usr/bin/clang-cpp-${LLVM} diff --git a/packaging/Dockerfile.ubuntu-gcc b/packaging/Dockerfile.ubuntu-gcc new file mode 100644 index 0000000..9361533 --- /dev/null +++ b/packaging/Dockerfile.ubuntu-gcc @@ -0,0 +1,30 @@ +FROM ubuntu:24.04 + +RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y \ + cmake \ + g++ \ + gfortran \ + git \ + vim \ + lldb \ + hdf5-tools \ + libboost-dev \ + libfftw3-dev \ + libgfortran5 \ + libgmp-dev \ + libhdf5-dev \ + libopenblas-dev \ + libopenmpi-dev \ + openmpi-bin \ + openmpi-common \ + openmpi-doc \ + python3-dev \ + python3-mako \ + python3-matplotlib \ + python3-mpi4py \ + python3-numpy \ + python3-pip \ + python3-scipy + +ENV PYTHON_VERSION=3.12 \ + CC=gcc CXX=g++ diff --git a/packaging/Dockerfile.ubuntu-intel b/packaging/Dockerfile.ubuntu-intel new file mode 100644 index 0000000..940d95b --- /dev/null +++ b/packaging/Dockerfile.ubuntu-intel @@ -0,0 +1,34 @@ +FROM intel/hpckit:2024.2.1-0-devel-ubuntu22.04 +ARG LLVM=18 + +RUN apt-get update && apt-get install -y lsb-release wget software-properties-common && \ + wget -O /tmp/llvm.sh https://apt.llvm.org/llvm.sh && chmod +x /tmp/llvm.sh && /tmp/llvm.sh ${LLVM} && \ + DEBIAN_FRONTEND=noninteractive apt-get install -y \ + g++-12 \ + git \ + vim \ + lldb-${LLVM} \ + hdf5-tools \ + libboost-dev \ + libclang-${LLVM}-dev \ + libc++-${LLVM}-dev \ + libc++abi-${LLVM}-dev \ + libfftw3-dev \ + libgmp-dev \ + libhdf5-dev \ + python3-clang-${LLVM} \ + python3-dev \ + python3-mako \ + python3-matplotlib \ + python3-numpy \ + python3-pip \ + python3-scipy \ + python3-venv + +ENV PYTHON_VERSION=3.10 \ + CC=icx CXX=icpx CXXFLAGS="-stdlib=libc++" \ + CPLUS_INCLUDE_PATH=/usr/lib/llvm-${LLVM}/include/c++/v1 \ + VIRTUAL_ENV=/home/venv \ + PATH=/home/venv/bin:$PATH + +RUN python3 -m venv --system-site-packages $VIRTUAL_ENV && pip install mpi4py cmake diff --git a/packaging/TRIQS-app4triqs-foss-2021b.eb.in b/packaging/app4triqs-foss-2021b.eb.in similarity index 94% rename from packaging/TRIQS-app4triqs-foss-2021b.eb.in rename to packaging/app4triqs-foss-2021b.eb.in index 384c781..5bf9f7e 100644 --- a/packaging/TRIQS-app4triqs-foss-2021b.eb.in +++ b/packaging/app4triqs-foss-2021b.eb.in @@ -1,6 +1,6 @@ easyblock = 'CMakeMake' -name = 'TRIQS-app4triqs' +name = 'app4triqs' version = '@PROJECT_VERSION@' homepage = 'https://triqs.github.io/app4triqs/' @@ -9,7 +9,7 @@ description = """ """ docurls = ['https://triqs.github.io/app4triqs/%(version_major_minor)s.x/'] -software_license = 'LicenseGPLv3' +software_license = 'LicenseApache2' toolchain = {'name': 'foss', 'version': '2021b'} toolchainopts = {'pic': True, 'usempi': True} @@ -27,7 +27,6 @@ dependencies = [ ('GMP', '6.2.1'), ('HDF5', '1.10.7'), ('Mako', '1.1.4'), - ('TRIQS', '3.3.0'), ('NFFT', '3.5.2') ] diff --git a/packaging/conda/build.sh b/packaging/conda/build.sh index 740a84d..2532460 100644 --- a/packaging/conda/build.sh +++ b/packaging/conda/build.sh @@ -10,8 +10,6 @@ export OMPI_MCA_rmaps_base_oversubscribe=yes export OMPI_MCA_btl_vader_single_copy_mechanism=none mpiexec="mpiexec --allow-run-as-root" -source $PREFIX/share/triqs/triqsvars.sh - cmake \ -DCMAKE_INSTALL_PREFIX=$PREFIX \ -DCMAKE_BUILD_TYPE=Release \ diff --git a/packaging/conda/meta.yaml.in b/packaging/conda/meta.yaml.in index bad6e1c..1b14c68 100644 --- a/packaging/conda/meta.yaml.in +++ b/packaging/conda/meta.yaml.in @@ -19,16 +19,12 @@ requirements: - {{ compiler('c') }} - {{ compiler('cxx') }} host: - - triqs {{ '.'.join(version.split('.')[:2]) }} - - boost-cpp - hdf5 - {{ mpi }} - libblas - liblapack - python run: - - {{ pin_compatible("triqs", max_pin="x.x") }} - - boost-cpp - hdf5 - {{ mpi }} - libblas @@ -46,8 +42,8 @@ test: about: home: https://triqs.github.io/app4triqs - license: GPL-3.0-or-later - license_family: GPL + license: Apache-2.0 + license_family: Apache license_file: LICENSE.txt summary: 'An application based on the TRIQS library' diff --git a/packaging/hwloc.patch b/packaging/hwloc.patch new file mode 100644 index 0000000..6ac9b58 --- /dev/null +++ b/packaging/hwloc.patch @@ -0,0 +1,13 @@ +diff -ru include/private/cpuid-x86.h.orig include/private/cpuid-x86.h +index 2758afe04..8f7acd894 100644 +--- include/private/cpuid-x86.h.orig ++++ include/private/cpuid-x86.h +@@ -62,6 +62,8 @@ static __hwloc_inline void hwloc_x86_cpuid(unsigned *eax, unsigned *ebx, unsigne + #else /* HWLOC_HAVE_MSVC_CPUIDEX */ + /* Note: gcc might want to use bx or the stack for %1 addressing, so we can't + * use them :/ */ ++ /* MSAN FIX */ ++ *ebx = *edx = 0; + #ifdef HWLOC_X86_64_ARCH + hwloc_uint64_t sav_rbx; + __asm__( diff --git a/python/app4triqs/CMakeLists.txt b/python/app4triqs/CMakeLists.txt index 753f314..12c3dad 100644 --- a/python/app4triqs/CMakeLists.txt +++ b/python/app4triqs/CMakeLists.txt @@ -10,9 +10,9 @@ foreach(file ${python_sources}) endforeach() # Install python files to proper location -set(PYTHON_LIB_DEST ${TRIQS_PYTHON_LIB_DEST_ROOT}/${PROJECT_NAME}) +set(PYTHON_LIB_DEST ${CPP2PY_PYTHON_LIB_DEST_ROOT}/${PROJECT_NAME}) install(FILES ${CMAKE_CURRENT_BINARY_DIR}/version.py DESTINATION ${PYTHON_LIB_DEST}) -install(DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} DESTINATION ${TRIQS_PYTHON_LIB_DEST_ROOT} FILES_MATCHING PATTERN "*.py" PATTERN "*_desc.py" EXCLUDE) +install(DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} DESTINATION ${CPP2PY_PYTHON_LIB_DEST_ROOT} FILES_MATCHING PATTERN "*.py" PATTERN "*_desc.py" EXCLUDE) # Build and install any python modules foreach(gen ${wrap_generators}) @@ -21,6 +21,6 @@ foreach(gen ${wrap_generators}) get_filename_component(module_dir ${gen} DIRECTORY) add_cpp2py_module(NAME ${module_name} DIRECTORY ${module_dir}) add_library(${PROJECT_NAME}::${module_name} ALIAS ${module_name}) - target_link_libraries(${module_name} ${PROJECT_NAME}_c triqs_py) + target_link_libraries(${module_name} ${PROJECT_NAME}_c) install(TARGETS ${module_name} DESTINATION ${PYTHON_LIB_DEST}/${module_dir}) endforeach() diff --git a/python/app4triqs/app4triqs_module_desc.py b/python/app4triqs/app4triqs_module_desc.py index 161e72f..92b3335 100644 --- a/python/app4triqs/app4triqs_module_desc.py +++ b/python/app4triqs/app4triqs_module_desc.py @@ -1,5 +1,5 @@ # Generated automatically using the command : -# c++2py ../../c++/app4triqs/app4triqs.hpp -p --members_read_only -N app4triqs -a app4triqs -m app4triqs_module -o app4triqs_module --moduledoc="The app4triqs python module" -C triqs --cxxflags="-std=c++17" --target_file_only +# c++2py ../../c++/app4triqs/app4triqs.hpp -p --members_read_only -N app4triqs -a app4triqs -m app4triqs_module -o app4triqs_module --moduledoc="The app4triqs python module" --cxxflags="-std=c++17" --target_file_only from cpp2py.wrap_generator import * # The module diff --git a/python/app4triqs/version.py.in b/python/app4triqs/version.py.in index 2d63daf..475c61e 100644 --- a/python/app4triqs/version.py.in +++ b/python/app4triqs/version.py.in @@ -22,11 +22,10 @@ ################################################################################ version = "@PROJECT_VERSION@" -triqs_hash = "@TRIQS_GIT_HASH@" @PROJECT_NAME@_hash = "@PROJECT_GIT_HASH@" def show_version(): print("\nYou are using @PROJECT_NAME@ version %s\n"%version) def show_git_hash(): - print("\nYou are using @PROJECT_NAME@ git hash %s based on triqs git hash %s\n"%("@PROJECT_GIT_HASH@", triqs_hash)) + print("\nYou are using @PROJECT_NAME@ git hash %s\n"%("@PROJECT_GIT_HASH@")) diff --git a/share/CMakeLists.txt b/share/CMakeLists.txt index 8d258a5..46b4d8d 100644 --- a/share/CMakeLists.txt +++ b/share/CMakeLists.txt @@ -1,7 +1,6 @@ add_subdirectory(cmake) if(NOT IS_SUBPROJECT - AND NOT CMAKE_INSTALL_PREFIX STREQUAL TRIQS_ROOT AND NOT CMAKE_INSTALL_PREFIX STREQUAL "/usr" AND NOT CMAKE_INSTALL_PREFIX STREQUAL "/usr/local" ) diff --git a/share/app4triqs.modulefile.in b/share/app4triqs.modulefile.in index 2c9befe..6b6289d 100644 --- a/share/app4triqs.modulefile.in +++ b/share/app4triqs.modulefile.in @@ -20,10 +20,6 @@ proc ModulesHelp { } { puts stderr "Git hash: $git_hash" } -# You may need to edit the next line if the triqs module -# is installed under a different name in your setup. -prereq triqs/@TRIQS_VERSION@ - # Only one version of @PROJECT_NAME@ can be loaded at a time conflict $name diff --git a/share/cmake/Modules/Findsanitizer.cmake b/share/cmake/Modules/Findsanitizer.cmake new file mode 100644 index 0000000..5cafd8b --- /dev/null +++ b/share/cmake/Modules/Findsanitizer.cmake @@ -0,0 +1,138 @@ +# Copyright Nils Wentzell 2018 +# Distributed under the GNU GENERAL PUBLIC LICENSE Version 3.0. +# See accompanying file LICENSE or https://www.gnu.org/licenses/gpl-3.0.txt +# +# This cmake find module looks for the LLVM Sanitizer Runtime Librariies +# It sets up SANITIZER_RT_PRELOAD and ${COMPONENT}_RT_LIBRARY for each +# requested component. +# +# Use this module by invoking find_package with the form:: +# +# find_package(sanitizer [REQUIRED] [asan] [ubsan]) +# +# Results are reported in:: +# +# SANITIZER_RT_PRELOAD Environment setting to load all Sanitizer Runtime Libraries +# ${COMPONENT}_RT_LIBRARY Individual Sanitizer Runtime Library + +if(${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang") + execute_process(COMMAND ${CMAKE_CXX_COMPILER} -print-resource-dir + OUTPUT_VARIABLE clang_resource_dir OUTPUT_STRIP_TRAILING_WHITESPACE) + if(${CMAKE_SYSTEM_NAME} MATCHES "Darwin") + set(search_paths ${clang_resource_dir}/lib/darwin ${clang_resource_dir}/../) + set(suffix _osx_dynamic) + elseif(${CMAKE_SYSTEM_NAME} MATCHES "Linux") + set(search_paths ${clang_resource_dir}/lib/linux ${clang_resource_dir}/../) + set(suffix -${CMAKE_SYSTEM_PROCESSOR}) + else() + message(FATAL_ERROR "Unknown platform") + endif() + if(${CMAKE_CXX_COMPILER_VERSION} VERSION_GREATER_EQUAL 13.0.0) + execute_process(COMMAND ${CMAKE_CXX_COMPILER} -print-runtime-dir + OUTPUT_VARIABLE clang_runtime_dir OUTPUT_STRIP_TRAILING_WHITESPACE) + list(APPEND search_paths ${clang_runtime_dir}) + endif() +elseif(${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU") + execute_process(COMMAND ${CMAKE_CXX_COMPILER} -print-libgcc-file-name + OUTPUT_VARIABLE libgcc_file OUTPUT_STRIP_TRAILING_WHITESPACE) + get_filename_component(search_path ${libgcc_file} DIRECTORY) +else() + message(FATAL_ERROR "Sanitizer is not available for your compiler") +endif() + +set(sanitizer_rt_libraries ${SANITIZER_RT_LIBRARIES}) +set(required_vars "") + +foreach(component ${${CMAKE_FIND_PACKAGE_NAME}_FIND_COMPONENTS}) + if(${component} STREQUAL "msan" OR TARGET ${component}) + continue() + endif() + + string(TOUPPER ${component} COMPONENT) + if((${component} STREQUAL "ubsan") AND (${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang") AND ASAN_RT_LIBRARY) + set(component ubsan_minimal) + endif() + + set(prefix clang_rt.) + find_library(${COMPONENT}_RT_LIBRARY + NAMES ${prefix}${component} ${prefix}${component}_standalone ${prefix}${component}${suffix} ${prefix}${component}_standalone${suffix} + PATHS ${search_paths}) + mark_as_advanced(${COMPONENT}_RT_LIBRARY) + + # Imported target + add_library(lib${component}_rt SHARED IMPORTED) + set_property(TARGET lib${component}_rt PROPERTY IMPORTED_LOCATION ${${COMPONENT}_RT_LIBRARY}) + + if(${CMAKE_FIND_PACKAGE_NAME}_FIND_REQUIRED_${component}) + list(APPEND required_vars ${COMPONENT}_RT_LIBRARY) + endif() + if(DEFINED sanitizer_rt_libraries AND NOT ${COMPONENT}_RT_LIBRARY MATCHES sanitizer_rt_libraries) + string(APPEND sanitizer_rt_libraries :${${COMPONENT}_RT_LIBRARY}) + else() + set(sanitizer_rt_libraries ${${COMPONENT}_RT_LIBRARY}) + endif() +endforeach() + +if(${CMAKE_SYSTEM_NAME} MATCHES "Darwin") + set(preload_var DYLD_INSERT_LIBRARIES) +else() + set(preload_var LD_PRELOAD) +endif() + +set(SANITIZER_RT_LIBRARIES ${sanitizer_rt_libraries} CACHE INTERNAL "Runtime shared libraries needed to load the LLVM sanitizers") +mark_as_advanced(SANITIZER_RT_LIBRARIES) +set(SANITIZER_RT_PRELOAD ${preload_var}=${SANITIZER_RT_LIBRARIES} CACHE INTERNAL "Preload command for santitizer runtime libraries") +mark_as_advanced(SANITIZER_RT_PRELOAD) + +# ----- Create Interface Targets ----- + +# Address Sanitizer +if(${CMAKE_FIND_PACKAGE_NAME}_FIND_REQUIRED_asan AND NOT TARGET asan) + add_library(asan INTERFACE) + target_compile_options(asan INTERFACE -fsanitize=address -fno-omit-frame-pointer -ggdb3) + target_link_libraries(asan INTERFACE "-fsanitize=address -fno-omit-frame-pointer$<$: -fuse-ld=gold>") + if(NOT DEFINED ENV{ASAN_OPTIONS}) + message(WARNING "ASAN_OPTIONS is not set. Consider setting ASAN_OPTIONS=symbolize=1:detect_leaks=0:halt_on_error=1 when running tests") + endif() +endif() + +# Undefined Behavior Sanitizer +if(${CMAKE_FIND_PACKAGE_NAME}_FIND_REQUIRED_ubsan AND NOT TARGET ubsan) + add_library(ubsan INTERFACE) + target_compile_options(ubsan INTERFACE -fsanitize=undefined -fsanitize=float-divide-by-zero -fsanitize=float-cast-overflow -fno-omit-frame-pointer -ggdb3) + target_link_libraries(ubsan INTERFACE "-fsanitize=undefined -fsanitize=float-divide-by-zero -fsanitize=float-cast-overflow -fno-omit-frame-pointer$<$: -fuse-ld=gold>") + if(NOT DEFINED ENV{UBSAN_OPTIONS}) + message(WARNING "UBSAN_OPTIONS is not set. Consider setting UBSAN_OPTIONS=symbolize=1:print_stacktrace=1:halt_on_error=1 when running tests") + endif() +endif() + +# Memory Sanitizer +if(${CMAKE_FIND_PACKAGE_NAME}_FIND_REQUIRED_msan AND NOT TARGET msan) + if(${CMAKE_FIND_PACKAGE_NAME}_FIND_REQUIRED_asan OR ${CMAKE_FIND_PACKAGE_NAME}_FIND_REQUIRED_ubsan OR ${CMAKE_FIND_PACKAGE_NAME}_FIND_REQUIRED_tsan) + message(FATAL_ERROR "Memory Sanitizer cannot be used with other sanitizers") + endif() + add_library(msan INTERFACE) + target_compile_options(msan INTERFACE -fsanitize=memory -fsanitize-memory-track-origins=2 -fno-omit-frame-pointer -ggdb3) + target_link_libraries(msan INTERFACE "-fsanitize=memory -fsanitize-memory-track-origins=2 -fno-omit-frame-pointer$<$: -fuse-ld=gold>") + if(NOT DEFINED ENV{MSAN_OPTIONS}) + message(WARNING "MSAN_OPTIONS is not set. Consider setting MBSAN_OPTIONS=symbolize=1 when running tests") + endif() +endif() + +# Thread Sanitizer +if(${CMAKE_FIND_PACKAGE_NAME}_FIND_REQUIRED_tsan AND NOT TARGET tsan) + add_library(tsan INTERFACE) + target_compile_options(tsan INTERFACE -fsanitize=thread -fno-omit-frame-pointer -ggdb3) + target_link_libraries(tsan INTERFACE "-fsanitize=thread -fno-omit-frame-pointer$<$: -fuse-ld=gold>") + if(NOT DEFINED ENV{TSAN_OPTIONS}) + message(WARNING "TSAN_OPTIONS is not set. Consider setting TSAN_OPTIONS=symbolize=1 when running tests") + endif() +endif() + +# ------------------------------------ + +include(FindPackageHandleStandardArgs) +find_package_handle_standard_args("sanitizer" + REQUIRED_VARS SANITIZER_RT_PRELOAD ${required_vars} + FAIL_MESSAGE "Sanitizer Runtime Libraries not found! Consider installing for additional checks!" +) diff --git a/test/Dockerfile.msan b/test/Dockerfile.msan new file mode 100644 index 0000000..10754dc --- /dev/null +++ b/test/Dockerfile.msan @@ -0,0 +1,68 @@ +FROM ubuntu:disco +ENV LLVM_MAJOR_VERSION=9 +ENV APPNAME=myapp + +RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y \ + clang-${LLVM_MAJOR_VERSION} \ + cmake \ + g++ \ + gfortran \ + git \ + libblas-dev \ + libboost-all-dev \ + libclang-${LLVM_MAJOR_VERSION}-dev \ + libfftw3-dev \ + libgfortran3 \ + libgmp-dev \ + zlib1g-dev \ + intel-mkl \ + python-clang-${LLVM_MAJOR_VERSION} \ + python-dev \ + python-h5py \ + python-mako \ + python-matplotlib \ + python-numpy \ + python-scipy \ + python-sphinx \ + python-nbsphinx \ + python-pip + +ENV CC=clang-${LLVM_MAJOR_VERSION} CXX=clang++-${LLVM_MAJOR_VERSION} LLVM_VERSION=${LLVM_MAJOR_VERSION}.0.0 + +ADD http://releases.llvm.org/${LLVM_VERSION}/libcxx-${LLVM_VERSION}.src.tar.xz /tmp/ +ADD http://releases.llvm.org/${LLVM_VERSION}/libcxxabi-${LLVM_VERSION}.src.tar.xz /tmp/ +RUN mkdir /tmp/build && cd /tmp/build && \ + tar -C /tmp -xf /tmp/libcxx-${LLVM_VERSION}.src.tar.xz && \ + tar -C /tmp -xf /tmp/libcxxabi-${LLVM_VERSION}.src.tar.xz && \ + cmake /tmp/libcxxabi-${LLVM_VERSION}.src -DLLVM_CONFIG_PATH=/usr/bin/llvm-config-${LLVM_MAJOR_VERSION} -DCMAKE_INSTALL_PREFIX=/usr/lib/llvm-${LLVM_MAJOR_VERSION} -DLIBCXXABI_LIBCXX_PATH=/tmp/libcxx-${LLVM_VERSION}.src -DLLVM_USE_SANITIZER=Memory && make -j2 && make install && \ + rm -rf * && \ + cmake /tmp/libcxx-${LLVM_VERSION}.src -DLLVM_CONFIG_PATH=/usr/bin/llvm-config-${LLVM_MAJOR_VERSION} -DCMAKE_INSTALL_PREFIX=/usr/lib/llvm-${LLVM_MAJOR_VERSION} -DLIBCXX_CXX_ABI=libcxxabi -DLIBCXX_CXX_ABI_INCLUDE_PATHS=/tmp/libcxxabi-${LLVM_VERSION}.src/include -DLLVM_USE_SANITIZER=Memory && make -j2 install && \ + rm -rf /tmp/libcxx* /tmp/build +ENV CXXFLAGS="-stdlib=libc++ -fsanitize=memory" CFLAGS="-fsanitize=memory" LD_LIBRARY_PATH=/usr/lib/llvm-${LLVM_MAJOR_VERSION}/lib LDFLAGS="-fsanitize=memory" + +RUN update-alternatives --set liblapack.so-x86_64-linux-gnu /usr/lib/x86_64-linux-gnu/libmkl_rt.so && \ + update-alternatives --set libblas.so-x86_64-linux-gnu /usr/lib/x86_64-linux-gnu/libmkl_rt.so + +ADD https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.5/src/CMake-hdf5-1.10.5.tar.gz /tmp/ +RUN mkdir /tmp/build && cd /tmp/build && \ + tar -C /tmp -xf /tmp/CMake-hdf5-1.10.5.tar.gz && \ + cmake /tmp/CMake-hdf5-1.10.5/hdf5-1.10.5 -DCMAKE_INSTALL_PREFIX=/usr && make -j2 && make install && \ + rm -rf * && \ + rm -rf /tmp/CMake-hdf5-1.10.5* /tmp/build + +RUN useradd -m build + +ENV SRC=/src \ + BUILD=/home/build \ + INSTALL=/usr/local \ + PYTHONPATH=/usr/local/lib/python2.7/site-packages:${PYTHONPATH} \ + CMAKE_PREFIX_PATH=/usr/lib/cmake/${APPNAME}:${CMAKE_PREFIX_PATH} + +COPY . ${SRC}/${APPNAME} +WORKDIR ${BUILD}/${APPNAME} +RUN chown -R build ${SRC}/${APPNAME} . +USER build +RUN cmake $SRC/nda -DCMAKE_INSTALL_PREFIX=$INSTALL -DMSAN=ON -DPYTHON_EXECUTABLE=$(which python) +RUN make VERBOSE=1 -j8 +ENV MSAN_SYMBOLIZER_PATH=/usr/lib/llvm-${LLVM_MAJOR_VERSION}/bin/llvm-symbolizer CTEST_OUTPUT_ON_FAILURE=1 +RUN make test || true diff --git a/test/c++/basic.cpp b/test/c++/basic.cpp index aecf689..4629cd1 100644 --- a/test/c++/basic.cpp +++ b/test/c++/basic.cpp @@ -1,4 +1,4 @@ -#include +#include #include using namespace app4triqs; diff --git a/test/python/Basic.py b/test/python/Basic.py index c0472fc..d0eba90 100644 --- a/test/python/Basic.py +++ b/test/python/Basic.py @@ -4,7 +4,6 @@ from app4triqs import Toto, chain from h5 import * -from triqs.utility import mpi class test_toto(unittest.TestCase): @@ -16,26 +15,14 @@ def test_add(self): c=a+b self.assertEqual(c, b) - def test_h5(self): - + a=Toto(0) with HDFArchive("f.h5",'w') as A: A["a"] = a with HDFArchive("f.h5",'r') as A: a_read = A["a"] self.assertEqual(a, a_read) - - - def test_mpi(self): - - a=Toto(0) - - if mpi.is_master_node(): - a=Toto(1) - mpi.bcast(a) - - self.assertEqual(a, Toto(1)) class test_chain(unittest.TestCase): diff --git a/test/python/CMakeLists.txt b/test/python/CMakeLists.txt index aa9d877..bcb22bc 100644 --- a/test/python/CMakeLists.txt +++ b/test/python/CMakeLists.txt @@ -10,6 +10,6 @@ set(all_tests Basic) foreach(test ${all_tests}) get_filename_component(test_name ${test} NAME_WE) get_filename_component(test_dir ${test} DIRECTORY) - add_test(NAME Py_${test_name} COMMAND ${TRIQS_PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/${test_dir}/${test_name}.py WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/${test_dir}) - set_property(TEST Py_${test_name} APPEND PROPERTY ENVIRONMENT PYTHONPATH=${PROJECT_BINARY_DIR}/python:$ENV{PYTHONPATH} ${SANITIZER_RT_PRELOAD}) + add_test(NAME Py_${test_name} COMMAND ${CPP2PY_PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/${test_dir}/${test_name}.py WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/${test_dir}) + set_property(TEST Py_${test_name} APPEND PROPERTY ENVIRONMENT PYTHONPATH=${PROJECT_BINARY_DIR}/python:${h5_BINARY_DIR}/python:$ENV{PYTHONPATH} ${SANITIZER_RT_PRELOAD}) endforeach()