Merge branch 'python' into breaking_bonds

.clang-tidy

@@ -7,6 +7,8 @@ Checks: |
  -clang-analyzer-optin.mpi.MPI-Checker,
  -clang-analyzer-security.FloatLoopCounter,
  bugprone-*,
+ -bugprone-easily-swappable-parameters,
+ -bugprone-implicit-widening-of-multiplication-result,
  clang-analyzer-alpha.*,
  modernize-deprecated-headers,
  modernize-make-shared,
@@ -71,15 +73,15 @@ CheckOptions:
  - key: modernize-make-shared.IgnoreMacros
  value: '1'
  - key: modernize-make-shared.IncludeStyle
- value: '0'
+ value: 'llvm'
  - key: modernize-make-shared.MakeSmartPtrFunction
  value: 'std::make_shared'
  - key: modernize-make-shared.MakeSmartPtrFunctionHeader
  value: memory
  - key: modernize-make-unique.IgnoreMacros
  value: '1'
  - key: modernize-make-unique.IncludeStyle
- value: '0'
+ value: 'llvm'
  - key: modernize-make-unique.MakeSmartPtrFunction
  value: 'std::make_unique'
  - key: modernize-make-unique.MakeSmartPtrFunctionHeader

.cppcheck

@@ -0,0 +1,9 @@
+// clang-format off
+constParameter
+unusedFunction
+missingIncludeSystem
+noConstructor
+noExplicitConstructor
+redundantAssignment
+uselessAssignmentPtrArg
+preprocessorErrorDirective

.github/actions/build_and_check/action.yml

@@ -22,7 +22,7 @@ runs:
  pip3 install numpy cython h5py scipy
  shell: bash
  - run: |
- export myconfig=maxset with_cuda=false test_timeout=600 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=${{ inputs.ubsan }} check_skip_long=${{ inputs.check_skip_long }}
  bash maintainer/CI/build_cmake.sh
  shell: bash
  # This is a workaround for the unfortunate interaction of MacOS and OpenMPI 4

.gitlab-ci.yml

@@ -1,4 +1,4 @@
-image: docker.pkg.github.com/espressomd/docker/ubuntu-20.04:254edd4a9c6e4d7b557be73158e400f5794e4f99
+image: ghcr.io/espressomd/docker/ubuntu-20.04:254edd4a9c6e4d7b557be73158e400f5794e4f99
 
 stages:
  - prepare
@@ -127,7 +127,7 @@ no_rotation:
 ubuntu:wo-dependencies:
  <<: *global_job_definition
  stage: build
- image: docker.pkg.github.com/espressomd/docker/ubuntu-wo-dependencies:9ef2166b82d4c0eb258d17f5ec29f7bc39991f5d
+ image: ghcr.io/espressomd/docker/ubuntu-wo-dependencies:9ef2166b82d4c0eb258d17f5ec29f7bc39991f5d
  variables:
  myconfig: 'maxset'
  with_cuda: 'false'
@@ -145,7 +145,7 @@ ubuntu:wo-dependencies:
 debian:10:
  <<: *global_job_definition
  stage: build
- image: docker.pkg.github.com/espressomd/docker/debian:9ef2166b82d4c0eb258d17f5ec29f7bc39991f5d
+ image: ghcr.io/espressomd/docker/debian:9ef2166b82d4c0eb258d17f5ec29f7bc39991f5d
  variables:
  with_cuda: 'false'
  myconfig: 'maxset'
@@ -160,7 +160,7 @@ debian:10:
 fedora:34:
  <<: *global_job_definition
  stage: build
- image: docker.pkg.github.com/espressomd/docker/fedora:9ef2166b82d4c0eb258d17f5ec29f7bc39991f5d
+ image: ghcr.io/espressomd/docker/fedora:9ef2166b82d4c0eb258d17f5ec29f7bc39991f5d
  variables:
  with_cuda: 'false'
  myconfig: 'maxset'
@@ -201,7 +201,7 @@ clang-sanitizer:
 fast_math:
  <<: *global_job_definition
  stage: build
- image: docker.pkg.github.com/espressomd/docker/cuda:9ef2166b82d4c0eb258d17f5ec29f7bc39991f5d
+ image: ghcr.io/espressomd/docker/cuda:9ef2166b82d4c0eb258d17f5ec29f7bc39991f5d
  variables:
  CC: 'gcc-9'
  CXX: 'g++-9'
@@ -222,7 +222,7 @@ fast_math:
 cuda11-maxset:
  <<: *global_job_definition
  stage: build
- image: docker.pkg.github.com/espressomd/docker/cuda:9ef2166b82d4c0eb258d17f5ec29f7bc39991f5d
+ image: ghcr.io/espressomd/docker/cuda:9ef2166b82d4c0eb258d17f5ec29f7bc39991f5d
  variables:
  CC: 'gcc-9'
  CXX: 'g++-9'
@@ -488,7 +488,7 @@ run_doxygen:
  - docker
  - linux
 
-check_cuda_maxset_no_gpu:
+maxset_no_gpu:
  <<: *global_job_definition
  stage: additional_checks
  when: on_success
@@ -502,7 +502,7 @@ check_cuda_maxset_no_gpu:
  - docker
  - linux
 
-check_with_odd_no_of_processors:
+maxset_3_cores:
  <<: *global_job_definition
  stage: additional_checks
  when: on_success

CMakeLists.txt

@@ -77,6 +77,7 @@ option(WITH_STOKESIAN_DYNAMICS "Build with Stokesian Dynamics" OFF)
 option(WITH_BENCHMARKS "Enable benchmarks" OFF)
 option(WITH_VALGRIND_INSTRUMENTATION
  "Build with valgrind instrumentation markers" OFF)
+option(WITH_CPPCHECK "Run Cppcheck during compilation" OFF)
 if(CMAKE_CXX_COMPILER_ID MATCHES "Clang")
  option(WITH_CLANG_TIDY "Run Clang-Tidy during compilation" OFF)
 endif()
@@ -97,6 +98,7 @@ endif()
 option(WARNINGS_ARE_ERRORS "Treat warnings as errors during compilation" OFF)
 option(WITH_CCACHE "Use ccache compiler invocation." OFF)
 option(WITH_PROFILER "Enable profiler annotations." OFF)
+option(INSIDE_DOCKER "Enable when running inside Docker." OFF)
 set(TEST_TIMEOUT "300" CACHE STRING
  "Timeout in seconds for each testsuite test")
 
@@ -126,18 +128,22 @@ include(MyConfig)
 
 include(CheckCXXSourceCompiles)
 
-set(__PRETTYFUNC__ __func__)
-foreach(func_name __PRETTY_FUNCTION__ __FUNCTION__)
+# cross-platform macro to print the function name in error messages
+set(PRETTY_FUNCTION_EXTENSION __func__)
+
+# search for a supported compiler extension that prints the function name as
+# well as its list of arguments, return type and namespace
+foreach(func_name __PRETTY_FUNCTION__ __FUNCSIG__ __FUNCTION__)
  check_cxx_source_compiles(
  "
  #include <string>
  int main() { std::string(${func_name}); }
  " result${func_name})
  if(result${func_name})
- set(__PRETTYFUNC__ ${func_name})
+ set(PRETTY_FUNCTION_EXTENSION ${func_name})
  break()
  endif(result${func_name})
-endforeach(func_name __PRETTY_FUNCTION__ __FUNCTION__)
+endforeach()
 
 #
 # Libraries
@@ -270,6 +276,32 @@ endif(WITH_VALGRIND_INSTRUMENTATION)
 #
 
 find_package(MPI 3.0 REQUIRED)
+find_package(MpiexecBackend)
+
+# OpenMPI checks the number of processes against the number of CPUs
+if("${MPIEXEC_BACKEND_NAME}" STREQUAL "OpenMPI" AND "${MPIEXEC_BACKEND_VERSION}"
+ VERSION_GREATER_EQUAL 2.0.0)
+ set(MPIEXEC_OVERSUBSCRIBE "-oversubscribe")
+else()
+ set(MPIEXEC_OVERSUBSCRIBE "")
+endif()
+
+# OpenMPI cannot run two jobs in parallel in a Docker container, because the
+# same base folder is used to store the process ids of multiple jobs. Since the
+# base folder is deleted upon completion of a job, other jobs will fail when
+# attempting to create subdirectories in the base folder.
+# https://github.com/open-mpi/ompi/issues/8510
+if("${MPIEXEC_BACKEND_NAME}" STREQUAL "OpenMPI" AND INSIDE_DOCKER)
+ cmake_host_system_information(RESULT hostname QUERY HOSTNAME)
+ function(set_mpiexec_tmpdir)
+ set(MPIEXEC_TMPDIR --mca orte_tmpdir_base
+ "/tmp/ompi.${hostname}.$ENV{USER}.${ARGV0}" PARENT_SCOPE)
+ endfunction()
+else()
+ function(set_mpiexec_tmpdir)
+ set(MPIEXEC_TMPDIR "" PARENT_SCOPE)
+ endfunction()
+endif()
 
 #
 # Boost
@@ -322,9 +354,7 @@ target_compile_options(
  # disable warnings from -Wextra
  -Wno-sign-compare
  -Wno-unused-function
- -Wno-unused-variable
  -Wno-unused-parameter
- -Wno-missing-braces
  $<$<CXX_COMPILER_ID:GNU>:-Wno-clobbered>
  $<$<CXX_COMPILER_ID:Intel>:-wd592>)
 
@@ -421,6 +451,19 @@ if(WITH_CLANG_TIDY)
  set(CMAKE_CXX_CLANG_TIDY "${CLANG_TIDY_EXE};--extra-arg=--cuda-host-only")
 endif()
 
+if(WITH_CPPCHECK)
+ find_program(CMAKE_CXX_CPPCHECK NAMES cppcheck)
+ if(NOT CMAKE_CXX_CPPCHECK)
+ message(FATAL_ERROR "Could not find the program cppcheck.")
+ endif()
+ list(APPEND CMAKE_CXX_CPPCHECK "--enable=all"
+ "--std=c++${CMAKE_CXX_STANDARD}" "--quiet" "--inline-suppr"
+ "--suppressions-list=${CMAKE_CURRENT_SOURCE_DIR}/.cppcheck")
+ if(WARNINGS_ARE_ERRORS)
+ list(APPEND CMAKE_CXX_CPPCHECK "--error-exitcode=2")
+ endif()
+endif()
+
 #
 # Testing
 #

cmake/FindMpiexecBackend.cmake

@@ -0,0 +1,48 @@
+#
+# Copyright (C) 2022 The ESPResSo project
+#
+# This file is part of ESPResSo.
+#
+# ESPResSo is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# ESPResSo is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+#
+
+# Find the MPI backend.
+#
+# This code sets the following variables:
+#
+# MPIEXEC_BACKEND_NAME MPIEXEC_BACKEND_VERSION
+
+set(MPIEXEC_BACKEND_NAME "unknown")
+set(MPIEXEC_BACKEND_VERSION 0.0.0)
+
+execute_process(
+ COMMAND ${MPIEXEC} --version RESULT_VARIABLE mpi_version_result
+ OUTPUT_VARIABLE mpi_version_output ERROR_VARIABLE mpi_version_output)
+if(mpi_version_result EQUAL 0)
+ if(mpi_version_output MATCHES "Intel\\(R\\) MPI Library")
+ set(MPIEXEC_BACKEND_NAME "Intel")
+ string(REGEX REPLACE ".*Build ([0-9]+).*" "\\1" MPIEXEC_BACKEND_VERSION ${mpi_version_output})
+ endif()
+ if(mpi_version_output MATCHES "HYDRA")
+ set(MPIEXEC_BACKEND_NAME "MPICH")
+ string(REGEX REPLACE ".*Version: +([0-9\\.]+).*" "\\1" MPIEXEC_BACKEND_VERSION ${mpi_version_output})
+ endif()
+ if(mpi_version_output MATCHES "\\(Open(RTE| MPI)\\)")
+ set(MPIEXEC_BACKEND_NAME "OpenMPI")
+ string(REGEX REPLACE ".*\\(Open(RTE| MPI)\\) ([0-9\\.]+).*" "\\2" MPIEXEC_BACKEND_VERSION ${mpi_version_output})
+ endif()
+endif()
+
+include( FindPackageHandleStandardArgs )
+FIND_PACKAGE_HANDLE_STANDARD_ARGS(MpiexecBackend REQUIRED_VARS MPIEXEC)

cmake/FindPythonHeaders.cmake

@@ -19,14 +19,14 @@
 # find the Python C++ headers
 execute_process(
  COMMAND ${PYTHON_EXECUTABLE} -c
- "import distutils.sysconfig as cg; print(cg.get_python_inc())"
+ "import sysconfig; print(sysconfig.get_path('include'))"
  OUTPUT_VARIABLE PYTHON_INCLUDE_DIRS OUTPUT_STRIP_TRAILING_WHITESPACE)
 # find Python installation directory
 if(NOT PYTHON_INSTDIR)
  execute_process(
  COMMAND
  ${PYTHON_EXECUTABLE} -c
- "import distutils.sysconfig as cg; print(cg.get_python_lib(prefix='${CMAKE_INSTALL_PREFIX}', plat_specific=True, standard_lib=False).replace('${CMAKE_INSTALL_PREFIX}/', '', 1))"
+ "import sysconfig; print(sysconfig.get_path('purelib', vars={'base': ''}).lstrip('/'))"
  OUTPUT_VARIABLE PYTHON_INSTDIR OUTPUT_STRIP_TRAILING_WHITESPACE)
 endif(NOT PYTHON_INSTDIR)
 

cmake/cmake_config.cmakein

@@ -23,7 +23,9 @@
 
 #define PACKAGE_NAME "${PROJECT_NAME}"
 
-#define __PRETTYFUNC__ @__PRETTYFUNC__@
-
-
-
+/**
+ * @brief Compiler-specific macro containing the demangled name
+ * of the function in the current scope. When the current compiler
+ * doesn't provide such an extension, defaults to @c __func__.
+ */
+#define PRETTY_FUNCTION_EXTENSION @PRETTY_FUNCTION_EXTENSION@

cmake/unit_test.cmake

@@ -1,17 +1,3 @@
-if(EXISTS ${MPIEXEC})
- # OpenMPI 2.0 and higher checks the number of processes against the number of
- # CPUs
- execute_process(
- COMMAND ${MPIEXEC} --version RESULT_VARIABLE mpi_version_result
- OUTPUT_VARIABLE mpi_version_output ERROR_VARIABLE mpi_version_output)
- if(mpi_version_result EQUAL 0 AND mpi_version_output MATCHES
- "\\(Open(RTE| MPI)\\) ([2-9]\\.|1[0-9])")
- set(MPIEXEC_OVERSUBSCRIBE "-oversubscribe")
- else()
- set(MPIEXEC_OVERSUBSCRIBE "")
- endif()
-endif()
-
 # unit_test function
 function(UNIT_TEST)
  cmake_parse_arguments(TEST "" "NAME;NUM_PROC" "SRC;DEPENDS" ${ARGN})
@@ -30,10 +16,11 @@ function(UNIT_TEST)
  if(${TEST_NUM_PROC} GREATER ${TEST_NP})
  set(TEST_NUM_PROC ${TEST_NP})
  endif()
-
+ set_mpiexec_tmpdir("${TEST_NAME}")
  add_test(${TEST_NAME} ${MPIEXEC} ${MPIEXEC_OVERSUBSCRIBE}
  ${MPIEXEC_NUMPROC_FLAG} ${TEST_NUM_PROC} ${MPIEXEC_PREFLAGS}
- ${CMAKE_CURRENT_BINARY_DIR}/${TEST_NAME} ${MPIEXEC_POSTFLAGS})
+ ${MPIEXEC_TMPDIR} ${CMAKE_CURRENT_BINARY_DIR}/${TEST_NAME}
+ ${MPIEXEC_POSTFLAGS})
  else()
  add_test(${TEST_NAME} ${TEST_NAME})
  endif()

doc/sphinx/advanced_methods.rst

@@ -1707,7 +1707,7 @@ In the *forward* reaction, the appropriate number of reactants (given by
 :math:`\nu_i`) is removed from the system, and the concomitant number of
 products is inserted into the system. In the *backward* reaction,
 reactants and products exchange their roles. The acceptance probability
-:math:`P^{\xi}` for move from state :math:`o` to :math:`n` reaction
+:math:`P^{\xi}` for a move from state :math:`o` to :math:`n` in the reaction
 ensemble is given by the criterion :cite:`smith94c`
 
 .. math::
@@ -1718,10 +1718,11 @@ ensemble is given by the criterion :cite:`smith94c`
 
 where :math:`\Delta E=E_\mathrm{new}-E_\mathrm{old}` is the change in potential energy,
 :math:`V` is the simulation box volume,
-and :math:`\beta=1/k_\mathrm{B}T`.
-The extent of reaction, :math:`\xi=1` for the forward, and
+:math:`\beta=1/k_\mathrm{B}T` is the Boltzmann factor, and
+:math:`\xi` is the extent of reaction, with :math:`\xi=1` for the forward and
 :math:`\xi=-1` for the backward direction.
-The parameter :math:`\Gamma` proportional to the reaction constant. It is defined as
+
+:math:`\Gamma` is proportional to the reaction constant. It is defined as
 
 .. math::
 

doc/sphinx/inter_bonded.rst

@@ -231,13 +231,13 @@ A virtual bond can be instantiated via
 :class:`espressomd.interactions.Virtual`::
 
  import espressomd.interactions
- tab = espressomd.interactions.Virtual()
+ vb = espressomd.interactions.Virtual()
 
 
 This creates a virtual bond type identifier for a pair bond
 without associated potential or force. It can be used to specify topologies
 and for some analysis that rely on bonds, or for bonds that should be
-displayed in the visualization.
+displayed in the visualizer.