Merge branch 'python' into python

espressomd · Sep 30, 2022 · 3f3b7a8 · 3f3b7a8
2 parents e7cee0c + 21c23c5
commit 3f3b7a8
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diff --git a/.github/actions/build_and_check/action.yml b/.github/actions/build_and_check/action.yml
@@ -9,10 +9,6 @@ inputs:
     description: 'Whether to build with undefined behavior sanitizer'
     required: true
     default: 'false'
-  check_skip_long:  # id of input
-    description: 'Whether to skip long python tests'
-    required: true
-    default: 'false'
 runs:
   using: "composite"
   steps:
@@ -22,7 +18,7 @@ runs:
        pip3 install numpy cython h5py scipy
       shell: bash
     - run: |
-        export myconfig=maxset with_cuda=false test_timeout=800 with_asan=${{ inputs.asan }} with_ubsan=${{ inputs.ubsan }} check_skip_long=${{ inputs.check_skip_long }}
+        export myconfig=maxset with_cuda=false test_timeout=800 with_asan=${{ inputs.asan }} with_ubsan=${{ inputs.ubsan }} check_skip_long=true build_procs=2 check_procs=2
         bash maintainer/CI/build_cmake.sh
       shell: bash
       # This is a workaround for the unfortunate interaction of MacOS and OpenMPI 4

diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml
@@ -4,6 +4,9 @@ on:
   schedule:
     - cron: '0 7 * * *'
 
+permissions:
+  contents: read # to fetch code (actions/checkout)
+
 jobs:
   deploy_docs:
     runs-on: ubuntu-20.04

diff --git a/.github/workflows/push_pull.yml b/.github/workflows/push_pull.yml
@@ -6,6 +6,9 @@ on:
   schedule:
     - cron: '0 3 * * *'
 
+permissions:
+  contents: read # to fetch code (actions/checkout)
+
 jobs:
   regular_check:
     runs-on: macos-latest
@@ -22,9 +25,12 @@ jobs:
         with:
           asan: false
           ubsan: false
-          check_skip_long: false
 
   sanitizer_check:
+    permissions:
+      contents: read # to fetch code (actions/checkout)
+      issues: write # to create an issue
+
     runs-on: macos-latest
     if: (github.event_name == 'schedule' && github.repository == 'espressomd/espresso')
     steps:
@@ -39,7 +45,6 @@ jobs:
         with:
           asan: true
           ubsan: true
-          check_skip_long: true
       - name: Setting job link variable
         if: ${{ failure() }}
         run: |

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
@@ -438,6 +438,8 @@ empty:
      with_static_analysis: 'true'
      with_scafacos: 'false'
      with_stokesian_dynamics: 'false'
+     with_coverage: 'false'
+     with_coverage_python: 'true'
   script:
     - bash maintainer/CI/build_cmake.sh
   tags:

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -54,8 +54,8 @@ minimal_compiler_version("Intel" 18.0)
 minimal_compiler_version("IntelLLVM" 2021.0)
 
 include(FeatureSummary)
-include(GNUInstallDirs)
 project(ESPResSo)
+include(GNUInstallDirs)
 include(option_enum)
 if(POLICY CMP0074)
   # make find_package() use <PackageName>_ROOT variables
@@ -162,7 +162,7 @@ foreach(func_name __PRETTY_FUNCTION__ __FUNCSIG__ __FUNCTION__)
 endforeach()
 
 #
-# Libraries
+# Interface libraries
 #
 
 # CUDA compiler
@@ -188,25 +188,49 @@ if(WITH_CUDA)
   endif()
 endif(WITH_CUDA)
 
-find_package(PythonInterp 3.8 REQUIRED)
-
+# Python interpreter and Cython interface library
 if(WITH_PYTHON)
+  find_package(Python 3.8 REQUIRED COMPONENTS Interpreter Development NumPy)
   find_package(Cython 0.29.14 REQUIRED)
-  find_package(PythonHeaders REQUIRED)
-  find_package(NumPy REQUIRED)
   find_program(IPYTHON_EXECUTABLE NAMES jupyter ipython3 ipython)
 endif(WITH_PYTHON)
 
+#
+# Installation folders
+#
+
+string(REGEX REPLACE "/+$" "" CMAKE_INSTALL_PREFIX "${CMAKE_INSTALL_PREFIX}")
+
+# folder for binaries and wrapper scripts
+set(ESPRESSO_INSTALL_BINDIR "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_BINDIR}")
+
+# folder for C++ and CUDA shared objects
+set(ESPRESSO_INSTALL_LIBDIR "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_LIBDIR}")
+
+# python site-packages, can be overriden with CMake options
+if(WITH_PYTHON)
+  if(NOT ESPRESSO_INSTALL_PYTHON)
+    if(CMAKE_INSTALL_PREFIX STREQUAL "/")
+      set(ESPRESSO_INSTALL_PYTHON "${Python_SITEARCH}")
+    else()
+      set(ESPRESSO_INSTALL_PYTHON
+          "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_LIBDIR}/python${Python_VERSION_MAJOR}.${Python_VERSION_MINOR}/site-packages"
+      )
+    endif()
+  endif()
+  # override: package C++, CUDA and Cython shared objects together
+  set(ESPRESSO_INSTALL_LIBDIR "${ESPRESSO_INSTALL_PYTHON}/espressomd")
+endif()
+
+#
+# Libraries
+#
+
 find_package(FFTW3)
 if(FFTW3_FOUND)
   set(FFTW 3)
 endif(FFTW3_FOUND)
 
-# If we build Python bindings, turn on script interface
-if(WITH_PYTHON)
-  set(WITH_SCRIPT_INTERFACE ON)
-endif()
-
 # We need the parallel hdf5 version!
 if(WITH_HDF5)
   # The FindHDF5 function will fall back to the serial version if no parallel
@@ -263,8 +287,7 @@ if(GSL_FOUND)
 endif(GSL_FOUND)
 
 if(WITH_STOKESIAN_DYNAMICS)
-  set(CMAKE_INSTALL_LIBDIR
-      "${CMAKE_INSTALL_PREFIX}/${PYTHON_INSTDIR}/espressomd")
+  set(CMAKE_INSTALL_LIBDIR "${ESPRESSO_INSTALL_LIBDIR}")
   include(FetchContent)
   FetchContent_Declare(
     stokesian_dynamics
@@ -337,7 +360,7 @@ find_package(Boost 1.69.0 REQUIRED ${BOOST_COMPONENTS})
 # Paths
 #
 
-set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/${PYTHON_INSTDIR}/espressomd")
+set(CMAKE_INSTALL_RPATH "${ESPRESSO_INSTALL_LIBDIR}")
 
 #
 # Flags
@@ -346,25 +369,25 @@ set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/${PYTHON_INSTDIR}/espressomd")
 # drop 'lib' prefix from all libraries
 set(CMAKE_SHARED_LIBRARY_PREFIX "")
 
-add_library(Espresso_coverage_flags INTERFACE)
-add_library(Espresso::coverage_flags ALIAS Espresso_coverage_flags)
+add_library(espresso_coverage_flags INTERFACE)
+add_library(espresso::coverage_flags ALIAS espresso_coverage_flags)
 if(WITH_COVERAGE)
   if(CMAKE_CXX_COMPILER_ID MATCHES "Clang")
     target_compile_options(
-      Espresso_coverage_flags INTERFACE -g -fprofile-instr-generate
+      espresso_coverage_flags INTERFACE -g -fprofile-instr-generate
                                         -fcoverage-mapping)
   else()
     target_compile_options(
-      Espresso_coverage_flags INTERFACE -g --coverage -fprofile-arcs
+      espresso_coverage_flags INTERFACE -g --coverage -fprofile-arcs
                                         -ftest-coverage)
-    target_link_libraries(Espresso_coverage_flags INTERFACE gcov)
+    target_link_libraries(espresso_coverage_flags INTERFACE gcov)
   endif()
 endif()
 
-add_library(Espresso_cpp_flags INTERFACE)
-add_library(Espresso::cpp_flags ALIAS Espresso_cpp_flags)
+add_library(espresso_cpp_flags INTERFACE)
+add_library(espresso::cpp_flags ALIAS espresso_cpp_flags)
 target_compile_options(
-  Espresso_cpp_flags
+  espresso_cpp_flags
   INTERFACE
     -Wall
     -Wextra
@@ -374,8 +397,11 @@ target_compile_options(
     $<$<CXX_COMPILER_ID:Clang>:-Wextern-initializer>
     $<$<CXX_COMPILER_ID:Clang>:-Wrange-loop-analysis>
     -Wfloat-conversion
-    $<$<CXX_COMPILER_ID:Clang,AppleClang>:-Wimplicit-float-conversion>
+    $<$<CXX_COMPILER_ID:Clang,AppleClang,IntelLLVM>:-Wimplicit-float-conversion>
+    $<$<CXX_COMPILER_ID:Clang,AppleClang,IntelLLVM>:-Wunused-exception-parameter>
+    $<$<CXX_COMPILER_ID:Clang,AppleClang,IntelLLVM>:-Wmissing-variable-declarations>
     $<$<AND:$<CXX_COMPILER_ID:Clang>,$<VERSION_GREATER_EQUAL:$<CXX_COMPILER_VERSION>,11.0.0>>:-Wnon-c-typedef-for-linkage>
+    $<$<NOT:$<CXX_COMPILER_ID:Intel>>:-Wdelete-non-virtual-dtor>
     # disable warnings from -Wextra
     -Wno-sign-compare
     -Wno-unused-function
@@ -390,18 +416,18 @@ target_compile_options(
 # disable warning from -Wextra on ARM processors
 if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU" AND CMAKE_SYSTEM_PROCESSOR MATCHES
                                             "arm")
-  target_compile_options(Espresso_cpp_flags INTERFACE -Wno-psabi)
+  target_compile_options(espresso_cpp_flags INTERFACE -Wno-psabi)
 endif()
 
 # prevent 80-bit arithmetic on old Intel processors
 if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU" AND CMAKE_SIZEOF_VOID_P EQUAL 4
    AND CMAKE_SYSTEM_PROCESSOR MATCHES "[xX]86")
-  target_compile_options(Espresso_cpp_flags INTERFACE -ffloat-store)
+  target_compile_options(espresso_cpp_flags INTERFACE -ffloat-store)
 endif()
 
 # enable boost::variant with more than 20 types
 target_compile_options(
-  Espresso_cpp_flags INTERFACE -DBOOST_MPL_CFG_NO_PREPROCESSED_HEADERS
+  espresso_cpp_flags INTERFACE -DBOOST_MPL_CFG_NO_PREPROCESSED_HEADERS
                                -DBOOST_MPL_LIMIT_LIST_SIZE=30)
 
 set(CMAKE_MACOSX_RPATH TRUE)
@@ -417,22 +443,22 @@ if(WITH_ASAN AND WITH_MSAN)
 endif()
 if(WITH_ASAN)
   set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -g -O1")
-  target_compile_options(Espresso_cpp_flags INTERFACE -fsanitize=address
+  target_compile_options(espresso_cpp_flags INTERFACE -fsanitize=address
                                                       -fno-omit-frame-pointer)
-  target_link_libraries(Espresso_cpp_flags INTERFACE -fsanitize=address)
+  target_link_libraries(espresso_cpp_flags INTERFACE -fsanitize=address)
 endif()
 if(WITH_MSAN)
   set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -g -O1")
-  target_compile_options(Espresso_cpp_flags INTERFACE -fsanitize=memory
+  target_compile_options(espresso_cpp_flags INTERFACE -fsanitize=memory
                                                       -fno-omit-frame-pointer)
-  target_link_libraries(Espresso_cpp_flags INTERFACE -fsanitize=memory)
+  target_link_libraries(espresso_cpp_flags INTERFACE -fsanitize=memory)
 endif()
 if(WITH_UBSAN)
-  target_compile_options(Espresso_cpp_flags INTERFACE -fsanitize=undefined)
-  target_link_libraries(Espresso_cpp_flags INTERFACE -fsanitize=undefined)
+  target_compile_options(espresso_cpp_flags INTERFACE -fsanitize=undefined)
+  target_link_libraries(espresso_cpp_flags INTERFACE -fsanitize=undefined)
 endif()
 
-target_link_libraries(Espresso_cpp_flags INTERFACE Espresso::coverage_flags)
+target_link_libraries(espresso_cpp_flags INTERFACE espresso::coverage_flags)
 
 #
 # Static analysis

diff --git a/Readme.md b/Readme.md
@@ -1,3 +1,9 @@
+# Invitation to the ESPResSo Summer School 2022
+
+[![CECAM Flagship School registration link](https://img.shields.io/badge/CECAM%20Flagship%20School-Register%20Now-blue?style=for-the-badge)](https://www.cecam.org/workshop-details/1146)
+
+The summer school "Simulating the dynamics of soft matter with ESPResSo, PyStencils and LbmPy" will take place on October 10-14, 2022, in Stuttgart. Registration is now open on [CECAM](https://www.cecam.org/workshop-details/1146).
+
 # ESPResSo
 
 [![GitLab CI](https://gitlab.icp.uni-stuttgart.de/espressomd/espresso/badges/python/pipeline.svg)](https://gitlab.icp.uni-stuttgart.de/espressomd/espresso/commits/python)
@@ -56,7 +62,7 @@ walk you through the basic usage of ESPResSo. Advanced simulation
 methods are extensively documented, with examples and links to the
 relevant literature. Additional resources such as tutorials and
 doxygen documentation can be found on https://espressomd.github.io.
-The official website is http://espressomd.org/wordpress/.
+The official website is https://espressomd.org/wordpress/.
 
 ## Installation
 
@@ -74,7 +80,7 @@ to use 4.1.4.
 ### Join the community
 
 Please consider subscribing to our
-[mailing list](http://espressomd.org/wordpress/community-and-support/mailing-lists/)
+[mailing list](https://espressomd.org/wordpress/community-and-support/mailing-lists/)
 if you're actively using ESPResSo, as we occasionally need community
 feedback when making decisions on the future of specific features in
 upcoming releases. You'll also get notifications on bugfix releases.
@@ -83,7 +89,7 @@ upcoming releases. You'll also get notifications on bugfix releases.
 
 If you use ESPResSo to publish scientific results, we would ask you to
 acknowledge this usage by mentioning the software with its version number and
-[citing the relevant papers](http://espressomd.org/wordpress/about/please-cite-us/).
+[citing the relevant papers](https://espressomd.org/wordpress/about/please-cite-us/).
 A number of algorithms in ESPResSo are fairly advanced and unique to ESPResSo.
 The authors of these contributions kindly ask you to cite the relevant
 publications, as indicated in the documentation. For detailed instructions, see

diff --git a/cmake/FindCUDACompilerClang.cmake b/cmake/FindCUDACompilerClang.cmake
@@ -1,4 +1,5 @@
-# Copyright (C) 2009-2020 The ESPResSo project
+#
+# Copyright (C) 2009-2022 The ESPResSo project
 # Copyright (C) 2009,2010
 #   Max-Planck-Institute for Polymer Research, Theory Group
 #
@@ -28,8 +29,8 @@ if(NOT CMAKE_CXX_COMPILER_ID MATCHES "Clang")
   )
 endif()
 
-add_library(Espresso_cuda_flags INTERFACE)
-add_library(Espresso::cuda_flags ALIAS Espresso_cuda_flags)
+add_library(espresso_cuda_flags INTERFACE)
+add_library(espresso::cuda_flags ALIAS espresso_cuda_flags)
 
 function(detect_clang_cuda_path)
   execute_process(COMMAND ${CMAKE_CUDA_COMPILER} ${CMAKE_CXX_FLAGS} --verbose
@@ -47,7 +48,7 @@ function(detect_clang_cuda_path)
         if(CLANG_VERBOSE_OUTPUT MATCHES "Found CUDA installation")
           set(CLANG_VERBOSE_OUTPUT ${CLANG_VERBOSE_OUTPUT} PARENT_SCOPE)
           message(STATUS "Clang did not automatically detect a compatible CUDA library; adding compiler flag --cuda-path=${unix_cuda_path}")
-          target_compile_options(Espresso_cuda_flags INTERFACE "--cuda-path=${unix_cuda_path}")
+          target_compile_options(espresso_cuda_flags INTERFACE "--cuda-path=${unix_cuda_path}")
           return()
         endif()
       endif()
@@ -66,7 +67,7 @@ string(REGEX REPLACE "^.*Found CUDA installation: .* version ([0-9\.]+|unknown).
 message(STATUS "Found CUDA-capable host compiler: ${CMAKE_CUDA_COMPILER}")
 if(NOT CLANG_VERBOSE_OUTPUT MATCHES "Found CUDA installation" OR CUDA_VERSION STREQUAL "unknown")
   message(STATUS "Clang did not automatically detect a compatible CUDA library; adding compiler flag -Wno-unknown-cuda-version")
-  target_compile_options(Espresso_cuda_flags INTERFACE -Wno-unknown-cuda-version)
+  target_compile_options(espresso_cuda_flags INTERFACE -Wno-unknown-cuda-version)
   message(STATUS "Found CUDA version: ${CUDAToolkit_VERSION}")
   message(STATUS "Found CUDA installation: ${CUDAToolkit_LIBRARY_DIR}")
 else()
@@ -75,7 +76,7 @@ else()
      CUDA_VERSION VERSION_GREATER_EQUAL "11.0" AND
      CUDA_VERSION VERSION_LESS "12.0")
     message(STATUS "Clang ${CMAKE_CXX_COMPILER_VERSION} doesn't natively support CUDA ${CUDAToolkit_VERSION_MAJOR}.${CUDAToolkit_VERSION_MINOR}; adding compiler flag -Wno-unknown-cuda-version")
-    target_compile_options(Espresso_cuda_flags INTERFACE -Wno-unknown-cuda-version)
+    target_compile_options(espresso_cuda_flags INTERFACE -Wno-unknown-cuda-version)
   endif()
   message(STATUS "Found CUDA version: ${CUDAToolkit_VERSION} (recognized by Clang as ${CUDA_VERSION})")
   message(STATUS "Found CUDA installation: ${CUDA_DIR}")
@@ -84,16 +85,17 @@ set(CUDA_VERSION ${CUDAToolkit_VERSION})
 set(CUDA 1)
 
 target_compile_options(
-  Espresso_cuda_flags
+  espresso_cuda_flags
   INTERFACE
   $<$<STREQUAL:${CMAKE_BUILD_TYPE},Debug>:-g>
   $<$<STREQUAL:${CMAKE_BUILD_TYPE},Release>:-O3 -DNDEBUG>
   $<$<STREQUAL:${CMAKE_BUILD_TYPE},MinSizeRel>:-O2 -DNDEBUG>
   $<$<STREQUAL:${CMAKE_BUILD_TYPE},RelWithDebInfo>:-O2 -g -DNDEBUG>
   $<$<STREQUAL:${CMAKE_BUILD_TYPE},Coverage>:-O3 -g>
   $<$<STREQUAL:${CMAKE_BUILD_TYPE},RelWithAssert>:-O3 -g>
-  $<$<VERSION_LESS:${CMAKE_CUDA_COMPILER_VERSION},11>:--cuda-gpu-arch=sm_30>
-  --cuda-gpu-arch=sm_52
+  $<$<VERSION_LESS:${CMAKE_CUDA_COMPILER_VERSION},12>:--cuda-gpu-arch=sm_52> # GTX-900 series (Maxwell)
+  $<$<VERSION_GREATER_EQUAL:${CMAKE_CUDA_COMPILER_VERSION},12>:--cuda-gpu-arch=sm_61> # GTX-1000 series (Pascal)
+  $<$<VERSION_GREATER_EQUAL:${CMAKE_CUDA_COMPILER_VERSION},12>:--cuda-gpu-arch=sm_75> # RTX-2000 series (Turing)
 )
 
 function(add_gpu_library)
@@ -107,7 +109,7 @@ function(add_gpu_library)
   set_source_files_properties(${TARGET_SOURCES} PROPERTIES LANGUAGE "CXX")
   add_library(${ARGV})
   set_target_properties(${TARGET_NAME} PROPERTIES LINKER_LANGUAGE "CXX")
-  target_link_libraries(${TARGET_NAME} PRIVATE Espresso::cuda_flags)
+  target_link_libraries(${TARGET_NAME} PRIVATE espresso::cuda_flags)
 endfunction()
 
 include(FindPackageHandleStandardArgs)