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Christian Ponte
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Version 2
-Improve AVX implementations -Improve base implementations to allow for autovectorization -Improve CMake project organisation -Add support for RAW files -Improve documentation -Move automated tests from Travis to Github Actions -Improve tests -Add single-threaded benchmarks -Move from C++14 to C++17
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‎.github/scripts/build_and_test.sh

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#!/usr/bin/env bash
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set -xe
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# Load env vars
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source ./.github/vars/$(echo ${GH_MATRIX_CC} | cut -d'+' -f1).sh
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source ./.github/vars/$(echo ${GH_MATRIX_CC} | cut -d'+' -f2).sh
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# Declare configurations
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declare -A cmake_config=(\
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["icelake-server"]="\
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512,popcnt-512,512,\
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64,,64,"\
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["cascadelake"]="\
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512,harley-seal-512,,\
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512,lookup-512,,\
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512,cpu-256,,\
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512,harley-seal-256,,\
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512,lookup-original-256,,\
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512,lookup-256,,\
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512,popcnt-movdq-64,,\
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512,popcnt-unrolled-errata-64,,\
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,,256,if-mask\
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64,,64,"\
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["haswell"]="\
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256,cpu-256,,\
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256,harley-seal-256,,\
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256,lookup-256,,\
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256,lookup-original-256,,\
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256,popcnt-movdq-64,,\
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256,popcnt-unrolled-errata-64,,\
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64,,64,")
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declare -A sde_arch_flag=(\
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["icelake-server"]="-icx"\
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["cascadelake"]="-clx"\
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["haswell"]="-hsw")
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src_dir=$(pwd)
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# Build loop
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mkdir build/
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cd build/
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for arch in ${!cmake_config[@]}; do
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for config in $(echo ${cmake_config[${arch}]}); do
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# Split config into vars
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gt_width=$(echo ${config} | cut -d',' -f1)
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popcnt_impl=$(echo ${config} | cut -d',' -f2)
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mi_width=$(echo ${config} | cut -d',' -f3)
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mi_impl=$(echo ${config} | cut -d',' -f4)
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# Compose CMake command
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cmake_args="-DCMAKE_BUILD_TYPE=RelWithDebInfo"
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if [ ! -z "$gt_width" ]; then
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cmake_args+=" -DGT_OP_WIDTH=${gt_width}"
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fi
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if [ ! -z "$popcnt_impl" ]; then
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cmake_args+=" -DPOPCNT_IMPL=${popcnt_impl}"
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fi
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if [ ! -z "$mi_width" ]; then
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cmake_args+=" -DMI_OP_WIDTH=${mi_width}"
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fi
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if [ ! -z "$mi_impl" ]; then
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cmake_args+=" -DMI_IMPL=${mi_impl}"
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fi
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# Build
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CFLAGS="${CFLAGS} -march=${arch} -mtune=${arch}" CXXFLAGS="${CFLAGS}" \
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cmake ${cmake_args} ${src_dir}
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make all
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# Test
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sde64 ${sde_arch_flag[${arch}]} -- \
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env CTEST_OUTPUT_ON_FAILURE=1 make test
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# Clean
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rm -rf *
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done
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done

‎.github/scripts/prep.sh

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#!/usr/bin/env bash
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set -xe
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# Load env vars
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source ./.github/vars/$(echo ${GH_MATRIX_CC} | cut -d'+' -f1).sh
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source ./.github/vars/$(echo ${GH_MATRIX_CC} | cut -d'+' -f2).sh
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# Install deps
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sudo apt-get -o Acquire::ForceIPv4=true update -qq 1>/dev/null
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sudo apt-get -o Acquire::ForceIPv4=true upgrade -qq 1>/dev/null
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sudo apt-get -o Acquire::ForceIPv4=true install \
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${COMPILER_PACKAGES} ${MPI_PACKAGES} -qq 1>/dev/null
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# Install Intel SDE
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INTEL_SDE_URL="https://software.intel.com/content/dam/develop/external/\
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us/en/documents/downloads/sde-external-8.69.1-2021-07-18-lin.tar.bz2"
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INTEL_SDE_TARFILE=$(echo ${INTEL_SDE_URL} | rev | cut -d '/' -f 1 | rev)
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wget -q --user-agent="Mozilla/5.0 (Windows NT 10.0; WOW64) AppleWebKit/537.36 \
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(KHTML, like Gecko) Chrome/51.0.2704.103 Safari/537.36" ${INTEL_SDE_URL}
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mkdir intel_sde/
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tar -xf ${INTEL_SDE_TARFILE} --strip-components=1 -C intel_sde/
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echo "$(pwd)/intel_sde" >> $GITHUB_PATH
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# Post install actions
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bash -c "${CC_POST_INSTALL}"
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bash -c "${MPI_POST_INSTALL}"

‎.github/vars/clang.sh

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export COMPILER_PACKAGES="clang-12 cmake"
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export CC=clang-12
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export CXX=clang++-12
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export CFLAGS="-O3 -ffast-math -Wall"
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export CXXFLAGS="${CFLAGS}"

‎.github/vars/gcc.sh

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export COMPILER_PACKAGES="gcc-10 g++-10 cmake"
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export CC=gcc-10
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export CXX=g++-10
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export CFLAGS="-O3 -ffast-math -Wall"
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export CXXFLAGS="${CFLAGS}"

‎.github/vars/intel.sh

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export COMPILER_PACKAGES="intel-basekit intel-hpckit cmake"
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export CC=icc
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export CXX=icpc
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export CFLAGS="-O3 -fp-model=fast -Wall"
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export CXXFLAGS="${CFLAGS}"
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# Add Intel repo
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APT_FILE=/etc/apt/sources.list.d/oneAPI.list
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if [ ! -f ${APT_FILE} ]; then
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wget -q "https://apt.repos.intel.com/intel-gpg-keys/\
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GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB"
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sudo apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
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rm GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
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echo "deb https://apt.repos.intel.com/oneapi all main" | sudo tee \
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${APT_FILE}
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fi
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# Load vars
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SETVARS_SH=/opt/intel/oneapi/setvars.sh
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if [ -f ${SETVARS_SH} ]; then
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{
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source ${SETVARS_SH}
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} 2>/dev/null
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fi
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# Also load vars after sucessfully installing the packages
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export CC_POST_INSTALL="\
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{\
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source '${SETVARS_SH}';\
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} 2>/dev/null"

‎.github/vars/intelmpi.sh

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export MPI_PACKAGES="intel-oneapi-mpi intel-oneapi-mpi-devel"
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export I_MPI_CC=${CC}
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export I_MPI_CXX=${CXX}
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export MPICC=mpiicc
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export MPICXX=mpiicpc
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# Add Intel repo
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APT_FILE=/etc/apt/sources.list.d/oneAPI.list
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if [ ! -f ${APT_FILE} ]; then
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wget -q "https://apt.repos.intel.com/intel-gpg-keys/\
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GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB"
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sudo apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
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rm GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
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echo "deb https://apt.repos.intel.com/oneapi all main" | sudo tee \
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${APT_FILE}
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fi

‎.github/vars/mpich.sh

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export MPI_PACKAGES="mpich libmpich12 libmpich-dev"
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export MPICH_CC=${CC}
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export MPICH_CXX=${CXX}
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export MPICC=mpicc
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export MPICXX=mpicxx

‎.github/vars/openmpi.sh

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export MPI_PACKAGES="openmpi-bin libopenmpi3 libopenmpi-dev"
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export OMPI_CC=${CC}
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export OMPI_CXX=${CXX}
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export MPICC=mpicc
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export MPICXX=mpic++
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# Fix openmpi complaining about not having enough slots
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OPENMPI_HOSTFILE=/etc/openmpi/openmpi-default-hostfile
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export MPI_POST_INSTALL="\
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if [ -z '$(cat ${OPENMPI_HOSTFILE} | grep -v -E '^#')' ]; then\
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echo \"localhost slots=32\" | sudo tee -a ${OPENMPI_HOSTFILE};\
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fi"

‎.github/workflows/ctest.yml

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name: CTest
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on:
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push:
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branches:
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- main
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- dev
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jobs:
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linux:
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runs-on: ubuntu-20.04
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strategy:
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matrix:
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cc: [gcc+openmpi, intel+intelmpi, clang+mpich]
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env:
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GH_MATRIX_CC: ${{ matrix.cc }}
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steps:
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- name: Display configuration
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run: |
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printenv
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lscpu
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- name: Checkout
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uses: actions/checkout@v1
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- name: Install dependencies
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run: ./.github/scripts/prep.sh
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- name: Build and test
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run: ./.github/scripts/build_and_test.sh

‎.readthedocs.yml

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‎.travis.yml

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This file was deleted.

‎CMakeLists.txt

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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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# 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 3.11)
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cmake_policy(SET CMP0074 NEW)
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project(Fiuncho VERSION 1 LANGUAGES CXX)
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set(CMAKE_CXX_STANDARD 14)
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project(Fiuncho VERSION 2 LANGUAGES CXX)
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set(CMAKE_CXX_STANDARD 17)
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set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/)
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set(CMAKE_STATIC_LIBRARY_PREFIX "")
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set(CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/cmake ${CMAKE_MODULE_PATH})

‎LICENSE.md

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### GNU GENERAL PUBLIC LICENSE
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## GNU GENERAL PUBLIC LICENSE
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Version 3, 29 June 2007
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@@ -673,3 +673,40 @@ library, you may consider it more useful to permit linking proprietary
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applications with the library. If this is what you want to do, use the
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GNU Lesser General Public License instead of this License. But first,
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please read <https://www.gnu.org/licenses/why-not-lgpl.html>.
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## THIRD PARTY SOFTWARE NOTICES
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Fiuncho contains third-party code governed by the license(s) indicated below:
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### sse-popcount (https://github.com/WojciechMula/sse-popcount/)
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Copyright (c) 2008-2016, Wojciech Muła
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Copyright (c) 2016, Kim Walisch
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Copyright (c) 2016, Dan Luu
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All rights reserved.
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Redistribution and use in source and binary forms, with or without
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modification, are permitted provided that the following conditions are
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met:
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1. Redistributions of source code must retain the above copyright
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notice, this list of conditions and the following disclaimer.
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2. Redistributions in binary form must reproduce the above copyright
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notice, this list of conditions and the following disclaimer in the
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documentation and/or other materials provided with the distribution.
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THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS
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IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
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TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
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PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
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HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED
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TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
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PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
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LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
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NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
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SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

‎README.md

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# Fiuncho
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3-
![](https://img.shields.io/badge/C++-14-blue.svg?style=flat&logo=c%2B%2B)
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![](https://img.shields.io/badge/C++-17-blue.svg?style=flat&logo=c%2B%2B)
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![](https://img.shields.io/github/license/UDC-GAC/fiuncho?color=blue)
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[![Build Status](https://travis-ci.com/UDC-GAC/fiuncho.svg?branch=main)](https://travis-ci.com/UDC-GAC/fiuncho)
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[![Documentation Status](https://readthedocs.org/projects/fiuncho/badge/?version=latest)](https://fiuncho.readthedocs.io/en/latest/?badge=latest)
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[![CTest](https://github.com/UDC-GAC/fiuncho/actions/workflows/ctest.yml/badge.svg)](https://github.com/UDC-GAC/fiuncho/actions/workflows/ctest.yml)
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[![Documentation Status](https://readthedocs.org/projects/fiuncho/badge/)](https://fiuncho.readthedocs.io/en/latest/)
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Fiuncho is an epistasis detection program, implementing an exhaustive search of
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epistasis interactions of any given size. Fiuncho offers multiple implementations,
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featuring AVX Intrinsics from different AVX extension sets, to support a wide
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variety of CPUs.
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epistasis interactions of any given size. Fiuncho uses a
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[SPMD](https://en.wikipedia.org/wiki/SPMD) (Single Program, Multiple Data)
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approach to accelerate the computation, exploiting the multiple cores available
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to a processor, or the multiple processors available in a cluster environment.
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Furthermore, Fiuncho takes advantage of the
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[SIMD](https://en.wikipedia.org/wiki/SIMD) (Single Instruction, Multiple Data)
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vector operations available to each CPU core, offering multiple *AVX*
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implementations to support a wide variety of *x86_64* processors.
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## Documentation
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‎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
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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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# 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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################################# Dependencies #################################
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include(FetchContent)

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