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Christian Ponte
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Create Fiuncho base project
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‎.gitignore

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.vscode/
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build/
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build/

‎.travis.yml

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branches:
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only:
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- master
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- dev
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language: cpp
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os: linux
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dist: bionic
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git:
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depth: false
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before_install:
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- sudo apt-get -q update
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script:
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- mkdir -p build
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- cd build
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- cmake -D CMAKE_BUILD_TYPE=Release ..
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- make fiuncho
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deploy:
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provider: pages
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skip_cleanup: true
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github_token: $GITHUB_TOKEN # Set in the settings page
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keep_history: true
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allow_empty_commit: true
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local_dir: build/docs/html
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on:
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branch: master
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# Build matrix
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jobs:
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include:
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# GCC + OpenMPI
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- compiler: gcc
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install:
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- sudo apt-get -y install cmake libopenmpi2 libopenmpi-dev
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after_success: skip
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# GCC + MPICH
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- compiler: gcc
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install:
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- sudo apt-get -y install cmake libmpich12 libmpich-dev
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after_success: skip
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# Clang + OpenMPI
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- compiler: clang
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env:
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- OMPI_CC=clang
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- OMPI_CXX=clang++
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install:
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- sudo apt-get -y install cmake libopenmpi2 libopenmpi-dev
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after_success: skip
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# Clang + MPICH
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- compiler: clang
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env:
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- MPICH_CC=clang
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- MPICH_CXX=clang++
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install:
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- sudo apt-get -y install cmake libmpich12 libmpich-dev
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after_success: skip
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# Docs build and deploy
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- install:
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- sudo apt-get -y install cmake python3-sphinx python3-breathe doxygen
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script:
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- mkdir -p build
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- cd build
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- cmake -D CMAKE_BUILD_TYPE=Release ..
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- make docs

‎CMakeLists.txt

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# MPI3SNP ~ https://github.com/chponte/mpi3snp
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# This file is part of Fiuncho.
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# Copyright (C) 2019 by Christian Ponte
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#
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# Fiuncho is free software: you can redistribute it and/or modify
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# it under the terms of the GNU General Public License as published by
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# the Free Software Foundation, either version 3 of the License, or
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# (at your option) any later version.
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#
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# Fiuncho is distributed in the hope that it will be useful,
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# but WITHOUT ANY WARRANTY; without even the implied warranty of
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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# GNU General Public License for more details.
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#
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# Copyright 2018 Christian Ponte
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#
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# Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated
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# documentation files (the "Software"), to deal in the Software without restriction, including without limitation the
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# rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to
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# permit persons to whom the Software is furnished to do so, subject to the following conditions:
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#
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# The above copyright notice and this permission notice shall be included in all copies or substantial portions of the
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# Software.
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#
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# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE
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# WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
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# COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
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# OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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# You should have received a copy of the GNU General Public License
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# along with Fiuncho. If not, see <http://www.gnu.org/licenses/>.
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############################### CMake variables ###############################
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cmake_minimum_required(VERSION 3.8)
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project(MPI3SNP VERSION 1.0)
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cmake_minimum_required(VERSION 3.11)
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project(Fiuncho VERSION 0.0.1 LANGUAGES CXX)
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set(CMAKE_CXX_STANDARD 14)
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set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/)
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set(CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/cmake ${CMAKE_MODULE_PATH})
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find_package(Threads REQUIRED)
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find_package(MPI REQUIRED)
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include(CheckLanguage)
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check_language(CUDA)
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############################# Build configuration #############################
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if (NOT DEFINED TARGET_ARCH)
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if (CMAKE_CUDA_COMPILER)
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set(TARGET_ARCH "GPU" CACHE STRING "Select target architecture")
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enable_language(CUDA)
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else ()
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set(TARGET_ARCH "CPU" CACHE STRING "Select target architecture")
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endif ()
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set_property(CACHE TARGET_ARCH PROPERTY STRINGS "CPU" "GPU")
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# Compiler configurations:
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# GNU
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if (CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
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set(CMAKE_CXX_FLAGS_DEBUG
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"-DDEBUG -g -fverbose-asm -O1 -march=native -mtune=native -Wall -Wextra\
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-Wpedantic")
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set(CMAKE_CXX_FLAGS_RELEASE
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"-DNDEBUG -Ofast -march=native -mtune=native")
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set(CMAKE_CXX_FLAGS_RELWITHDEBINFO
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"-DDEBUG -g -fverbose-asm -Ofast -march=native -mtune=native")
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# Intel
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elseif (CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
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set(CMAKE_CXX_FLAGS_DEBUG
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"-DDEBUG -g -debug inline-debug-info -O1 -xHost -mtune=native -Wall")
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set(CMAKE_CXX_FLAGS_RELEASE
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"-DNDEBUG -Ofast -xHost -mtune=native")
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set(CMAKE_CXX_FLAGS_RELWITHDEBINFO
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"-DDEBUG -g -debug inline-debug-info -Ofast -xHost -mtune=native")
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# Clang
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elseif (CMAKE_CXX_COMPILER_ID STREQUAL "Clang")
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set(CMAKE_CXX_FLAGS_DEBUG
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"-DDEBUG -g -fverbose-asm -O1 -march=native -mtune=native -Wall -Wextra\
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-Wpedantic")
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set(CMAKE_CXX_FLAGS_RELEASE
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"-DNDEBUG -Ofast -march=native -mtune=native")
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set(CMAKE_CXX_FLAGS_RELWITHDEBINFO
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"-DDEBUG -g -fverbose-asm -Ofast -march=native -mtune=native")
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else()
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message(FATAL_ERROR "Unsupported compiler detected: "
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${CMAKE_CXX_COMPILER})
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endif()
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# Build type configuration
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set(DEFAULT_BUILD_TYPE "Release")
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if (NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES)
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message(STATUS "Setting build type to ${DEFAULT_BUILD_TYPE} as none was specified.")
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set(CMAKE_BUILD_TYPE "${DEFAULT_BUILD_TYPE}" CACHE
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STRING "Choose the type of build" FORCE)
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message(STATUS
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"Setting build type to ${DEFAULT_BUILD_TYPE} as none was specified")
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set(CMAKE_BUILD_TYPE "${DEFAULT_BUILD_TYPE}"
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CACHE STRING "Choose the type of build" FORCE)
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# Set the possible values of build type for cmake-gui
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set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS "Debug" "Release")
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set_property(CACHE CMAKE_BUILD_TYPE
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PROPERTY STRINGS "Debug" "Release" "RelWithDebInfo")
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endif ()
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set(CMAKE_CXX_STANDARD 14)
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set(CMAKE_CXX_FLAGS_DEBUG "-g -O0")
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set(CMAKE_CXX_FLAGS_RELEASE "-DNDEBUG -O3")
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if (${TARGET_ARCH} STREQUAL "GPU")
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enable_language(CUDA)
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set(CMAKE_CUDA_STANDARD 11)
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set(CMAKE_CUDA_STANDARD_REQUIRED ON)
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set(CMAKE_CUDA_FLAGS "-arch=sm_30")
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set(CMAKE_CUDA_FLAGS_DEBUG "-g -O0")
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set(CMAKE_CUDA_FLAGS_RELEASE "-DNDEBUG -O3")
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# set(CUDA_PROPAGATE_HOST_FLAGS OFF)
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endif ()
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############################# Project directories #############################
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# Third party libraries (common to GPU and CPU builds)
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add_subdirectory(thirdparty)
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# Project documentation
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add_subdirectory(docs EXCLUDE_FROM_ALL)
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# Project sources
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add_subdirectory(src)
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add_subdirectory(app)

‎README.md

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# MPI3SNP
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# Fiuncho
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<p>
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<a href="https://doi.org/10.1177/1094342019852128" alt="Publication">
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<img src="https://img.shields.io/badge/DOI-10.1177%2F1094342019852128-blue"/></a>
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</p>
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[![Build Status](https://travis-ci.com/chponte/fiuncho.svg?token=Gxpcxy8NqxmoyEPxEuR5&branch=master)](https://travis-ci.com/chponte/fiuncho)
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## What is MPI3SNP?
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MPI3SNP is a parallel software tool dedicated to genome-wide association studies, performing a third-order exhaustive
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search. It is targeted to cluster architectures, and mitigates the cubic time complexity inherent to third-order
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searches by exploiting the several layers of parallelism present in a supercomputer. CPU and GPU implementations are
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offered.
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## Building
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Support is currently limited to linux distributions only.
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### Requirements
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* CMake (>3.0 version)
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* A C++14 compatible compiler
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* MPI library
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Optional:
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* CUDA
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### Compilation
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CMake is the project build manager. CMake should be able to determine installed compilers and libraries. If this is
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is not the case, please refer to your CMake version's documentation. By default, CMake will check for a CUDA
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installation and set the target architecture accordingly. This behaviour can be manually controlled by setting the
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`TARGET_ARCH` CMake variable to `CPU` or `GPU`.
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Building the sources looks like this:
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```commandline
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cd MPI3SNP/project/path
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mkdir build
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cd build/
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cmake ..
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make -j4
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```
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## Usage
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MPI3SNP takes two files as the input, using the [PLINK/TPED](https://www.cog-genomics.org/plink2/formats#tfam) format,
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and writes the results to a third file. All file paths are provided to the program as positional arguments as follows:
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```commandline
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./MPI3SNP <path/to/tped> <path/to/tfam> <path/to/output>
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```
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Additional configuration options (specific to either CPU or GPU implementation) are available to the user, and can be
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consulted using the `-h` flag.
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## Sample files
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[Sample files](https://github.com/chponte/mpi3snp/wiki/Sample-files) can be found on MPI3SNP's wiki. These are a syntetic dataset used for performance evaluation, which describe the input file format and can be used for verification/evaluation purposes.
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## Troubleshooting
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Support is currently limited to linux distributions only. If you are having trouble building/using the application,
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please submit a new issue to get help.
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## License
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This software is licensed under the GPU GPLv3 license. Check the [LICENSE](LICENSE.md) file for details.
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## WIP

‎app/CMakeLists.txt

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# This file is part of Fiuncho.
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#
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# Fiuncho is free software: you can redistribute it and/or modify
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# it under the terms of the GNU General Public License as published by
5+
# the Free Software Foundation, either version 3 of the License, or
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# (at your option) any later version.
7+
#
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# Fiuncho is distributed in the hope that it will be useful,
9+
# but WITHOUT ANY WARRANTY; without even the implied warranty of
10+
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
11+
# GNU General Public License for more details.
12+
#
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# You should have received a copy of the GNU General Public License
14+
# along with Fiuncho. If not, see <http://www.gnu.org/licenses/>.
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################################### Targets ###################################
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add_executable(fiuncho main.cpp)
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target_link_libraries(fiuncho PRIVATE fiuncho_lib)

‎src/main.cpp ‎app/main.cpp

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/*
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* MPI3SNP ~ https://github.com/chponte/mpi3snp
2+
* This file is part of Fiuncho.
33
*
4-
* Copyright 2018 Christian Ponte
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* Fiuncho is free software: you can redistribute it and/or modify
5+
* it under the terms of the GNU General Public License as published by
6+
* the Free Software Foundation, either version 3 of the License, or
7+
* (at your option) any later version.
58
*
6-
* Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated
7-
* documentation files (the "Software"), to deal in the Software without restriction, including without limitation the
8-
* rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to
9-
* permit persons to whom the Software is furnished to do so, subject to the following conditions:
9+
* Fiuncho is distributed in the hope that it will be useful,
10+
* but WITHOUT ANY WARRANTY; without even the implied warranty of
11+
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
12+
* GNU General Public License for more details.
1013
*
11-
* The above copyright notice and this permission notice shall be included in all copies or substantial portions of the
12-
* Software.
13-
*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE
15-
* WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
16-
* COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
17-
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
14+
* You should have received a copy of the GNU General Public License
15+
* along with Fiuncho. If not, see <https://www.gnu.org/licenses/>.
1816
*/
1917

2018
/**
@@ -27,9 +25,9 @@
2725
*/
2826

2927
#include <mpi.h>
30-
#include "IOMpi.h"
31-
#include "Search.h"
32-
#include "Node_information.h"
28+
#include <fiuncho/utils/IOMpi.h>
29+
#include <fiuncho/engine/Search.h>
30+
#include <fiuncho/utils/Node_information.h>
3331

3432
int main(int argc, char **argv) {
3533
MPI_Init(&argc, &argv);
@@ -82,7 +80,7 @@ int main(int argc, char **argv) {
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8381
delete search;
8482
// Print runtime statistics to stdout
85-
IOMpi::Instance().cprint<IOMpi::B>(statistics.To_string());
83+
IOMpi::Instance().cprint<IOMpi::B>(statistics.str());
8684
IOMpi::Instance().mprint<IOMpi::B>("Overall time: " + std::to_string(etime - stime) + " seconds\n");
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8886
MPI_Finalize();

‎cmake/FindSphinx.cmake

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find_program(SPHINX_EXECUTABLE NAMES sphinx-build
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HINTS
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$ENV{SPHINX_DIR}
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PATH_SUFFIXES bin
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DOC "Sphinx documentation generator"
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)
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include(FindPackageHandleStandardArgs)
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find_package_handle_standard_args(Sphinx DEFAULT_MSG
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SPHINX_EXECUTABLE
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)
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mark_as_advanced(SPHINX_EXECUTABLE)

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