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Merge pull request #136 from mir-group/develop
Phoebe 1.0 merge to master
2 parents 920f772 + 6123485 commit b894b1a

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‎.github/workflows/buildandtest.yml‎

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name: Build and Test
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on: [push, pull_request]
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jobs:
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build:
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strategy:
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matrix:
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omp: [OFF, ON]
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mpi: [OFF, ON]
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name: "(OpenMP, MPI) ="
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runs-on: ubuntu-20.04
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env:
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BUILD_DIR: build_${{ matrix.omp }}_${{ matrix.mpi }}
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OMP_NUM_THREADS: 4
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steps:
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- name: Install dependencies
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run: |
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sudo apt-get update
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sudo apt install -y libopenblas-dev liblapack-dev libhdf5-dev libhdf5-openmpi-dev libscalapack-openmpi-dev python3-pip -o Acquire::Retries=3 --fix-missing
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pip3 install numpy
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- name: Checkout
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uses: actions/checkout@v2
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with:
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submodules: true
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- name: Configure
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run: |
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mkdir ${BUILD_DIR}
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cd ${BUILD_DIR}
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cmake .. -DOMP_AVAIL=${{ matrix.omp }} -DKokkos_ENABLE_OPENMP=${{ matrix.omp }} -DMPI_AVAIL=${{ matrix.mpi }} -DHDF5_AVAIL=ON
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- name: Build
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run: |
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cd ${BUILD_DIR}
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make -j4
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make -j4 runTests
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- name: RunTests
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run : |
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cd ${BUILD_DIR}
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./runTests
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- name: Download test data
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run: |
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wget github.com/mir-group/phoebe-data/archive/master.zip
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unzip -j master.zip "phoebe-data-master/example/Silicon-ph/qe-phonons/*" -d "example/Silicon-ph/qe-phonons"
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unzip -j master.zip "phoebe-data-master/example/Silicon-ph/qe-ph-anharmonic/*" -d "example/Silicon-ph/qe-ph-anharmonic"
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unzip -j master.zip "phoebe-data-master/example/Silicon-el/qe-elph/*" -d "example/Silicon-el/qe-elph"
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unzip 'example/Silicon-el/qe-elph/silicon.phoebe.*.dat.zip' -d example/Silicon-el/qe-elph/
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cp example/Silicon-el/qe-elph/* example/Silicon-epa/qe-elph
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mkdir example/Silicon-epa/qe-elph/out
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unzip -j master.zip "phoebe-data-master/example/Silicon-epa/qe-elph/out/*" -d "example/Silicon-epa/qe-elph/out"
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- name: Run epa example without MPI
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working-directory: example/Silicon-epa
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run: |
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../../${BUILD_DIR}/phoebe -in qeToPhoebeEPA.in
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../../${BUILD_DIR}/phoebe -in epaTransport.in
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../../${BUILD_DIR}/phoebe -in electronFourierBands.in
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../../${BUILD_DIR}/phoebe -in electronFourierDos.in
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python3 reference/run_check.py
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- name: Run epa example with MPI
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working-directory: example/Silicon-epa
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if: matrix.mpi == 'ON'
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run: |
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mpirun -np 4 --oversubscribe ../../${BUILD_DIR}/phoebe -in epaTransport.in
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mpirun -np 4 --oversubscribe ../../${BUILD_DIR}/phoebe -in electronFourierBands.in
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mpirun -np 4 --oversubscribe ../../${BUILD_DIR}/phoebe -in electronFourierDos.in
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python3 reference/run_check.py
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- name: Run ph example without MPI
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working-directory: example/Silicon-ph
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run: |
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../../${BUILD_DIR}/phoebe -in phononTransport.in
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../../${BUILD_DIR}/phoebe -in phononBands.in
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../../${BUILD_DIR}/phoebe -in phononDos.in
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../../${BUILD_DIR}/phoebe -in phononLifetimes.in
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python3 reference/run_check.py
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- name: Run ph example with MPI
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working-directory: example/Silicon-ph
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if: matrix.mpi == 'ON'
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run: |
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mpirun -np 4 --oversubscribe ../../${BUILD_DIR}/phoebe -in phononTransport.in
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mpirun -np 4 --oversubscribe ../../${BUILD_DIR}/phoebe -in phononBands.in
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mpirun -np 4 --oversubscribe ../../${BUILD_DIR}/phoebe -in phononDos.in
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mpirun -np 4 --oversubscribe ../../${BUILD_DIR}/phoebe -in phononLifetimes.in
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python3 reference/run_check.py
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- name: Run el example without MPI
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working-directory: example/Silicon-el
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run: |
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../../${BUILD_DIR}/phoebe -in qeToPhoebeWannier.in
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../../${BUILD_DIR}/phoebe -in electronWannierTransport.in
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../../${BUILD_DIR}/phoebe -in electronWannierBands.in
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../../${BUILD_DIR}/phoebe -in electronWannierDos.in
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../../${BUILD_DIR}/phoebe -in electronLifetimes.in
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python3 reference/run_check.py
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- name: Run el example with MPI
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working-directory: example/Silicon-el
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if: matrix.mpi == 'ON'
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run: |
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# Note: don't run this as it runs out-of-memory on the VM
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#mpirun -np 4 --oversubscribe ../../${BUILD_DIR}/phoebe -in qeToPhoebeWannier.in
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mpirun -np 4 --oversubscribe ../../${BUILD_DIR}/phoebe -in electronWannierTransport.in
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mpirun -np 4 --oversubscribe ../../${BUILD_DIR}/phoebe -in electronWannierBands.in
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mpirun -np 4 --oversubscribe ../../${BUILD_DIR}/phoebe -in electronWannierDos.in
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mpirun -np 4 --oversubscribe ../../${BUILD_DIR}/phoebe -in electronLifetimes.in
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python3 reference/run_check.py
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mpirun -np 4 --oversubscribe ../../${BUILD_DIR}/phoebe -ps 2 -in electronWannierTransport.in
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mpirun -np 4 --oversubscribe ../../${BUILD_DIR}/phoebe -ps 2 -in electronLifetimes.in
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python3 reference/run_check.py
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‎.gitignore‎

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# Build folders
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*build*/
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# Output files
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*.json
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# Prerequisites
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*.d
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*phoebe
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#IDE files
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.project
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.project
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.pydevproject
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#MacOS specific files
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.DS_Store
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.Makefile.swp
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#CMake stuff:
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*CMakeCache.txt
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*CMakeFiles
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*cmake_install.cmake
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CMakeDoxy*
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Makefile
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CMakeLists.txt.orig
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CTestTestfile.cmake
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eigen_dep-prefix/
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epa_test/
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example/Silicon/log
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googletest/
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pugixml_dep-prefix/
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runTests*_include.cmake
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scalapack_dep-prefix/
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spglib_dep-prefix/
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runTests[1]_include.cmake
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runTests
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tags
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*.plist
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# Clion IDE
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.idea
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*zip
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# built by cmake for version number
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src/main.h

‎.gitmodules‎

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[submodule "lib/kokkos"]
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path = lib/kokkos
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url = https://github.com/kokkos/kokkos.git

‎CITATION.cff‎

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# YAML 1.2
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---
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authors:
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-
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affiliation: "Harvard University"
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family-names: Cepellotti
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given-names: Andrea
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-
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affiliation: "Harvard University"
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family-names: Coulter
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given-names: Jennifer
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-
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affiliation: "Harvard University"
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family-names: Johansson
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given-names: Anders
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-
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affiliation: "Harvard University"
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family-names: Fedorova
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given-names: Natalya
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-
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affiliation: "Harvard University"
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family-names: Kozinsky
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given-names: Boris
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cff-version: "1.1.0"
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license: "MIT License"
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message: "If you use this software, please cite it using these metadata."
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repository-code: "https://github.com/mir-group/phoebe"
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title: "Phoebe: a collection of Phonon and Electron Boltzmann Equation solvers"
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version: "1.0"
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...

‎CMakeLists.txt‎

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if(NOT CMAKE_BUILD_TYPE)
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set(CMAKE_BUILD_TYPE "Release" CACHE
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STRING "Choose the type of build." FORCE)
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endif(NOT CMAKE_BUILD_TYPE)
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if(Kokkos_ENABLE_CUDA)
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set(Kokkos_ENABLE_CUDA_LAMBDA ON CACHE BOOL "don't touch")
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set(CMAKE_CXX_COMPILER ${CMAKE_CURRENT_SOURCE_DIR}/lib/kokkos/bin/nvcc_wrapper)
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endif()
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cmake_minimum_required(VERSION 3.16)
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set(CMAKE_CXX_STANDARD 14)
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project(Phoebe LANGUAGES C CXX Fortran VERSION 1.0)
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configure_file(src/main.h.in ../src/main.h)
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## load custom cmake find_package
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set(CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake")
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if(CMAKE_CXX_COMPILER_ID MATCHES GNU)
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SET(GCC_COVERAGE_COMPILE_FLAGS "-Wall -Wextra -ggdb -fno-omit-frame-pointer -Wno-deprecated-copy -Wno-ignored-attributes")
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add_definitions(${GCC_COVERAGE_COMPILE_FLAGS})
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add_compile_options(-Wno-error=parentheses)
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endif()
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############ OPTIONS ################
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# these can be toggled in a build script by
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# supplying arguments to cmake like cmake -DHDF5_AVAIL=OFF ../
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option(MPI_AVAIL "Build with MPI wrappers" ON)
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option(OMP_AVAIL "Build with OMP" ON)
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option(HDF5_AVAIL "Build with HDF5" ON)
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option(HDF5_SERIAL "Force build to accomodate serial only HDF5, but still use MPI" OFF)
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option(BUILD_DOC "Build documentation" ON)
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############### SOURCE ###############
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FILE(GLOB_RECURSE SOURCE_FILES src src/*.cpp)
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list(REMOVE_ITEM SOURCE_FILES ${CMAKE_CURRENT_SOURCE_DIR}/src/main.cpp)
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message(${CMAKE_CURRENT_SOURCE_DIR})
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message(${SOURCE_FILES})
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FILE(GLOB TEST_SOURCES test/*.cpp test/interaction3ph/*.cpp)
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include_directories(src src/algebra src/apps src/bands src/bte src/constants src/harmonic src/interaction src/mpi src/observable src/parser src/points)
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include(lib/CMakeLists.txt)
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include(GoogleTest)
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add_executable(phoebe src/main.cpp ${SOURCE_FILES})
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add_executable(runTests ${TEST_SOURCES} ${SOURCE_FILES})
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set_target_properties(runTests PROPERTIES EXCLUDE_FROM_ALL TRUE)
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# dependencies
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add_dependencies(phoebe spglib_dep pugixml_dep eigen_dep)
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add_dependencies(runTests spglib_dep pugixml_dep eigen_dep)
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target_link_libraries(phoebe symspg pugixml kokkos nlohmann_json::nlohmann_json)
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enable_testing()
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target_link_libraries(runTests symspg pugixml gtest_main kokkos nlohmann_json::nlohmann_json)
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gtest_discover_tests(
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runTests
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WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}
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)
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################ PARALLEL ####################
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# build with MPI and scalapack
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if (MPI_AVAIL)
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find_package(MPI REQUIRED)
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target_link_libraries(phoebe MPI::MPI_CXX)
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target_link_libraries(runTests MPI::MPI_CXX)
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add_definitions("-DMPI_AVAIL") # this sets turns on ifdefs for mpi in the cpp
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find_library(SCALAPACK_LIB NAMES scalapack scalapack-openmpi mkl_scalapack_lp64 PATHS ENV LD_LIBRARY_PATH)
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if(${SCALAPACK_LIB} MATCHES NOTFOUND)
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ExternalProject_Add(scalapack_dep
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BINARY_DIR ${CMAKE_CURRENT_BINARY_DIR}/scalapack_build
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SOURCE_DIR ${CMAKE_CURRENT_BINARY_DIR}/scalapack_src
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GIT_REPOSITORY https://github.com/Reference-ScaLAPACK/scalapack.git
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INSTALL_COMMAND ""
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UPDATE_COMMAND ""
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CMAKE_ARGS
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-DCMAKE_BUILD_TYPE=Release
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-DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
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-DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}
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-DCMAKE_Fortran_COMPILER=${CMAKE_Fortran_COMPILER}
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)
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set(SCALAPACK_LIB scalapack)
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message(WARNING "No SCALAPACK library found in CMAKE_LIBRARY_PATH, building our own.")
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add_dependencies(phoebe scalapack_dep)
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else()
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if(${SCALAPACK_LIB} MATCHES mkl)
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if("${MPI_CXX_LIBRARIES}" MATCHES openmpi)
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find_library(BLACS_LIB NAMES mkl_blacs_openmpi_lp64 PATHS ENV LD_LIBRARY_PATH)
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elseif("${MPI_CXX_LIBRARIES}" MATCHES intel)
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find_library(BLACS_LIB NAMES mkl_blacs_intelmpi_lp64 PATHS ENV LD_LIBRARY_PATH)
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else()
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message(FATAL_ERROR "Confused by MPI library when looking for BLACS.")
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endif()
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if(${BLACS_LIB} MATCHES NOTFOUND)
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message(FATAL_ERROR "Found Intel SCALAPACK but not BLACS")
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endif()
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message(STATUS "Found BLACS: ${BLACS_LIB}")
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endif()
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message(STATUS "Found SCALAPACK: ${SCALAPACK_LIB}")
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endif()
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find_package(BLAS REQUIRED)
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find_package(LAPACK REQUIRED)
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include_directories(${BLAS_INCLUDE_DIR})
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include_directories(${LAPACK_INCLUDE_DIR})
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## Very important to link scalapack before blas and lapack
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target_link_libraries(phoebe ${SCALAPACK_LIB} ${BLACS_LIB} ${LAPACK_LIBRARIES} ${BLAS_LIBRARIES} -lgfortran)
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target_link_libraries(runTests ${SCALAPACK_LIB} ${BLACS_LIB} ${LAPACK_LIBRARIES} ${BLAS_LIBRARIES} -lgfortran)
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else()
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set(HDF5_SERIAL ON)
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## even for the serial version, we require lapack
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find_package(BLAS REQUIRED)
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find_package(LAPACK REQUIRED)
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include_directories(${BLAS_INCLUDE_DIR})
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include_directories(${LAPACK_INCLUDE_DIR})
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target_link_libraries(phoebe ${LAPACK_LIBRARIES} ${BLAS_LIBRARIES} -lgfortran)
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target_link_libraries(runTests ${LAPACK_LIBRARIES} ${BLAS_LIBRARIES} -lgfortran)
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endif()
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# build with openMP
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if(OMP_AVAIL)
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find_package(OpenMP)
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target_link_libraries(phoebe OpenMP::OpenMP_CXX)
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target_link_libraries(runTests OpenMP::OpenMP_CXX)
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add_definitions("-DOMP_AVAIL")
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endif()
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# build with HDF5
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if(HDF5_AVAIL)
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if(HDF5_SERIAL)
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add_definitions("-DHDF5_SERIAL")
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else()
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set(HDF5_PREFER_PARALLEL TRUE)
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endif()
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add_dependencies(phoebe highfive_dep)
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add_dependencies(runTests highfive_dep)
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find_package(HDF5 REQUIRED)
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target_link_libraries(phoebe ${HDF5_LIBRARIES})
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target_link_libraries(runTests ${HDF5_LIBRARIES})
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include_directories(${HDF5_INCLUDE_DIRS})
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add_definitions("-DHDF5_AVAIL")
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endif()
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############# DOCS ############
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find_package(Doxygen)
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find_package(Sphinx)
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IF (BUILD_DOC)
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IF (NOT DOXYGEN_FOUND)
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message("Doxygen need to be installed to generate the doxygen documentation")
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else()
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# set input and output files
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set(DOXYGEN_IN ${CMAKE_CURRENT_SOURCE_DIR}/doc/doxygen/Doxyfile)
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set(DOXYGEN_OUT ${CMAKE_CURRENT_BINARY_DIR}/doc/doxygen/Doxyfile.out)
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# request to configure the file
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configure_file(${DOXYGEN_IN} ${DOXYGEN_OUT} @ONLY)
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message("Doxygen configured")
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# note the option ALL which allows to build the docs together with the application
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add_custom_target(
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docDevel
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COMMAND ${DOXYGEN_EXECUTABLE} ${DOXYGEN_IN}
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WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/../doc/doxygen
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COMMENT "Generating API documentation with Doxygen"
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VERBATIM)
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IF (NOT SPHINX_FOUND)
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message("Documentation needs also sphinx")
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else()
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add_custom_target(
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doc
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COMMAND make html
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WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/../doc/sphinx
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COMMENT "Building user documentation with Sphinx"
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VERBATIM)
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add_dependencies(doc docDevel)
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endif()
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ENDIF()
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endif()
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