CMake development

.github/workflows/CI.yml

@@ -5,8 +5,9 @@ on:
     branches: [ master ]
   pull_request:
     branches: [ master ]
-  schedule:
-    - cron: "0 0 * * *"
+# don't run the CRON part in my fork
+#  schedule:
+#    - cron: "0 0 * * *"
 
   workflow_dispatch:
 

.github/workflows/run_cmake.yaml

@@ -0,0 +1,83 @@
+# This workflow carries out the build of the package with CMake
+
+name: CMake build
+
+on:
+  push:
+  workflow_dispatch:
+
+jobs:
+  build-GNU:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Install dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install gfortran libopenmpi-dev cmake python3-dev pip
+          pip install scipy matplotlib getdist anesthetic ipython mpi4py
+
+      - name: Run CMake
+        run: cmake -B build
+
+      - name: Build
+        run: make -C build install
+
+      - name: Test pypolychord
+        run: python run_pypolychord.py
+
+      - name: Test pypolychord (MPI)
+        run: mpirun -np 2 python run_pypolychord.py
+
+  build-Intel:
+    runs-on: ubuntu-latest
+    container:
+      image: intel/oneapi-hpckit
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Run CMake
+        run: cmake -B build -DCMAKE_Fortran_COMPILER=ifort -DCMAKE_CXX_COMPILER=icpc
+
+      - name: Build
+        run: make -C build install
+
+      - name: Test pypolychord
+        run: python run_pypolychord.py
+
+      - name: Test pypolychord (MPI)
+        run: mpirun -np 2 python run_pypolychord.py
+
+  build-MacOS:
+    runs-on: macos-latest
+    strategy:
+      matrix:
+        cc: [ gcc, clang ]
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Install dependencies
+        run: |
+          brew install cmake gcc openmpi
+          pip3 install numpy scipy matplotlib getdist anesthetic ipython mpi4py
+
+      - name: Run CMake - GCC
+        if: ${{ env.cc == 'gcc' }}
+        run: cmake -B build -DCMAKE_Fortran_COMPILER=gfortran-11 -DCMAKE_CXX_COMPILER=gcc-11
+
+      - name: Run CMake - AppleClang
+        if: ${{ env.cc == 'clang' }}
+        run: cmake -B build -DCMAKE_Fortran_COMPILER=gfortran-11
+
+      - name: Build
+        run: make -C build install
+
+      - name: Test pypolychord
+        run: python run_pypolychord.py
+
+      - name: Test pypolychord (MPI)
+        run: mpirun -np 2 python run_pypolychord.py

CMakeLists.txt

@@ -0,0 +1,145 @@
+cmake_minimum_required(VERSION 3.4)
+
+project(PolyChordLite Fortran)
+
+# languages
+enable_language(CXX)
+enable_language(Fortran)
+
+# options
+option(MPI "Build with MPI" ON)
+option(python "Build PyPolyChord package" ON)
+option(python_user_install "Install Python package for user (--user)" ON)
+
+# enforce matching of the CXX and Fortran compilers
+if (NOT "${CMAKE_Fortran_COMPILER_ID}" MATCHES "${CMAKE_CXX_COMPILER_ID}"
+        AND NOT ("${CMAKE_Fortran_COMPILER_ID}" MATCHES "GNU" AND
+        "${CMAKE_CXX_COMPILER_ID}" MATCHES "AppleClang"))
+    message(FATAL_ERROR "You need to use the same vendor for your C++ and Fortran compiler")
+endif ()
+
+# flags for all three compiler types
+# todo: inspect the flags and implement in a nicer way
+if ("${CMAKE_Fortran_COMPILER_ID}" MATCHES "Intel")
+    message("Using INTEL compilers")
+
+    set(CMAKE_Fortran_FLAGS "-fpp -fpic -assume noold_maxminloc -heap-arrays -ipo -O3 -no-prec-div -xHost -w -vec-report0 -qopt-report0")
+    set(CMAKE_CXX_FLAGS "-std=c++11 -fpic -ipo -O3 -no-prec-div -xHost -w -vec-report0 -qopt-report0")
+
+    add_compile_options("-nofor-main")
+    link_libraries("-nofor-main")
+
+elseif ("${CMAKE_Fortran_COMPILER_ID}" MATCHES "GNU")
+    message("Using GNU compilers")
+
+    set(CMAKE_Fortran_FLAGS "-ffree-line-length-none -cpp -fPIC -fno-stack-arrays -Ofast")
+    set(CMAKE_CXX_FLAGS "-std=c++11 -fPIC -Ofast")
+
+    # for GitHub actions MacOS -- debug only
+    add_compile_options("-lstdc++")
+    link_libraries("-lstdc++")
+
+    if (CMAKE_Fortran_COMPILER_VERSION VERSION_GREATER 10.0)
+        # GCC 10 is complaining about MPI interfaces, turn this to warnings
+        SET(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -fallow-argument-mismatch")
+    endif ()
+
+elseif ("${CMAKE_Fortran_COMPILER_ID}" MATCHES "Cray")
+    message("Using Cray compilers")
+
+    set(CMAKE_Fortran_FLAGS "-fpp -fpic -qopenmp -dynamic")
+    set(CMAKE_CXX_FLAGS "-fpic -qopenmp -dynamic")
+
+endif ()
+
+# find MPI & link to everything from now on
+if (MPI)
+    find_package(MPI REQUIRED)
+    message(STATUS "MPI_Fortran_COMPILER: ${MPI_Fortran_COMPILER}")
+    link_libraries(MPI::MPI_Fortran)
+    link_libraries(MPI::MPI_CXX)
+
+    # definitions
+    add_compile_definitions(USE_MPI)
+endif (MPI)
+
+# this will be module building directory, allows linking
+set(CMAKE_Fortran_MODULE_DIRECTORY ${PROJECT_BINARY_DIR}/generated/mods)
+
+# on installation we get this prefix as well
+set(CMAKE_INSTALL_PREFIX ${PROJECT_BINARY_DIR})
+
+# target directories -> stuff installed in these directories
+set(target_lib_dir ${PROJECT_SOURCE_DIR}/lib)
+set(target_bin_dir ${PROJECT_SOURCE_DIR}/bin)
+
+# directories where we want to make things
+add_subdirectory(src)
+add_subdirectory(likelihoods)
+
+if (python)
+    #################################################################
+    # The Compiled .so file
+    #################################################################
+
+    # PyPolyChord stuff
+    message(STATUS "Enabling Python package build")
+    find_package(Python3 COMPONENTS Interpreter Development NumPy REQUIRED)
+
+    # find out the suffix for the current python version
+    EXECUTE_PROCESS(
+            COMMAND ${Python3_EXECUTABLE} "-c" "import sysconfig;print(sysconfig.get_config_var('EXT_SUFFIX'))"
+            OUTPUT_VARIABLE python_so_suffix
+    )
+    STRING(REPLACE "\n" "" python_so_suffix ${python_so_suffix})
+    message(STATUS "Python shared object suffix is: ${python_so_suffix}")
+
+    # the extension module
+    add_library(_pypolychord SHARED pypolychord/_pypolychord.cpp $<TARGET_OBJECTS:objlib_chord>)
+    set_target_properties(_pypolychord
+            PROPERTIES
+            OUTPUT_NAME _pypolychord
+            PREFIX ""
+            SUFFIX "${python_so_suffix}"
+            )
+    # dependencies and includes
+    target_link_libraries(_pypolychord Python3::Python Python3::NumPy)
+    target_include_directories(_pypolychord PUBLIC src/polychord) # PolyChord headers for python extensions
+
+    # remember the place of this
+    set(target_python_so ${CMAKE_CURRENT_BINARY_DIR}/_pypolychord${python_so_suffix})
+
+    # place all outputs in one place
+    install(TARGETS _pypolychord
+            LIBRARY DESTINATION ${target_lib_dir})
+
+    #################################################################
+    # The simple python module
+    #################################################################
+
+    # hack ofr version
+    set(PACKAGE_VERSION "1.18.2")
+
+    set(SETUP_PY_IN "${CMAKE_CURRENT_SOURCE_DIR}/setup_cmake_template.py")
+    set(SETUP_PY "${CMAKE_CURRENT_BINARY_DIR}/setup.py")
+    set(DEPS "${CMAKE_CURRENT_SOURCE_DIR}/pypolychord/__init__.py")
+    set(OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/build/timestamp") # dummy target for dependence
+
+    # fill in the variables of the setup.py file
+    configure_file(${SETUP_PY_IN} ${SETUP_PY})
+
+    # custom target
+    add_custom_command(OUTPUT ${OUTPUT}
+            COMMAND ${Python3_EXECUTABLE} ${SETUP_PY} build
+            COMMAND ${CMAKE_COMMAND} -E touch ${OUTPUT}
+            DEPENDS ${DEPS} _pypolychord)
+    add_custom_target(target ALL DEPENDS ${OUTPUT})
+
+    # installation with setup.py
+    if (python_user_install)
+        install(CODE "execute_process(COMMAND ${Python3_EXECUTABLE} ${SETUP_PY} install)")
+    else (python_user_install)
+        install(CODE "execute_process(COMMAND ${Python3_EXECUTABLE} ${SETUP_PY} install --user)")
+    endif (python_user_install)
+
+endif (python)

Makefile

@@ -44,7 +44,7 @@ endif
 
 
 ifeq ($(MPI),1)
-FFLAGS += -DMPI
+FFLAGS += -DUSE_MPI
 CXXFLAGS += -DUSE_MPI
 endif
 

README.rst

@@ -5,8 +5,7 @@
    :target: https://arxiv.org/abs/1506.00171
    :alt: Open-access paper
 
-PolyChord v 1.20.1
-
+PolyChord v 1.21.0
 Will Handley, Mike Hobson & Anthony Lasenby
 
 [email protected]

devtools/docker_gnu/Dockerfile

@@ -0,0 +1,40 @@
+FROM ubuntu:latest
+MAINTAINER "Tamas K Stenczel <[email protected]>"
+
+# Time Zone data
+ARG DEBIAN_FRONTEND=noninteractive
+ENV TZ=Europe/London
+
+RUN apt-get -q update && \
+    apt-get -qy install --no-install-recommends \
+        # general
+        make \
+        gfortran \
+        libopenmpi-dev \
+        libblas-dev \
+        liblapack-dev \
+        libfftw3-3  \
+        # cmake and tools
+        cmake vim git wget ca-certificates \
+        g++ \
+        python3-dev pip \
+    && rm -rf /var/lib/apt/lists/*
+
+RUN pip3 install scipy matplotlib getdist anesthetic ipython mpi4py
+
+# reinstall newer cmake, same as in the Intel image
+ARG cmake_url=https://github.com/Kitware/CMake/releases/download/v3.20.0/cmake-3.20.0-linux-x86_64.sh
+ADD $cmake_url /
+RUN file=$(basename "$cmake_url") && \
+   bash $file --prefix=/usr --skip-license && \
+   rm $file
+
+# DEV use: oh-my-zsh instead of bash
+# Uses "robbyrussell" theme (original Oh My Zsh theme), with no plugins
+RUN sh -c "$(wget -O- https://github.com/deluan/zsh-in-docker/releases/download/v1.1.1/zsh-in-docker.sh)" -- \
+    -t robbyrussell
+ENTRYPOINT "/usr/bin/zsh"
+WORKDIR /work
+
+# python executable
+RUN echo "alias python=python3" >> /root/.zshrc