4.2.1rc

.clang-tidy

@@ -5,11 +5,11 @@ Checks: |
    -clang-analyzer-core.NullDereference,
    -clang-analyzer-core.uninitialized.UndefReturn,
    -clang-analyzer-optin.mpi.MPI-Checker,
-   -clang-analyzer-security.FloatLoopCounter,
    bugprone-*,
    -bugprone-easily-swappable-parameters,
    -bugprone-implicit-widening-of-multiplication-result,
    -bugprone-macro-parentheses,
+   -bugprone-reserved-identifier,
    clang-analyzer-alpha.*,
    modernize-deprecated-headers,
    modernize-make-shared,

.codecov.yml

@@ -30,7 +30,7 @@ coverage:
     patch:
       default:
         enabled: yes
-        threshold: 1%
+        threshold: 2%
     changes: no
 
 parsers:

.github/actions/build_and_check/action.yml

@@ -9,20 +9,16 @@ 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:
     - run: |
        brew install boost boost-mpi fftw
        brew install hdf5-mpi
-       pip3 install numpy cython h5py scipy
+       pip3 install -c requirements.txt 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
         bash maintainer/CI/build_cmake.sh
       shell: bash
       # This is a workaround for the unfortunate interaction of MacOS and OpenMPI 4

.github/workflows/deploy.yml

@@ -4,16 +4,19 @@ on:
   schedule:
     - cron: '0 7 * * *'
 
+permissions:
+  contents: read # to fetch code (actions/checkout)
+
 jobs:
   deploy_docs:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     if: github.repository == 'espressomd/espresso'
     environment: deploy_documentation
     steps:
       - name: Install pandoc
-        uses: r-lib/actions/setup-pandoc@v1
+        uses: r-lib/actions/setup-pandoc@v2
       - name: Setup SSH agent
-        uses: webfactory/ssh-agent@v0.5.2
+        uses: webfactory/ssh-agent@v0.7.0
         with:
           ssh-private-key: ${{ secrets.GH_PAGES_SSH_PRIVATE_KEY }}
       - name: Checkout

.github/workflows/push_pull.yml

@@ -6,40 +6,45 @@ on:
   schedule:
     - cron: '0 3 * * *'
 
+permissions:
+  contents: read # to fetch code (actions/checkout)
+
 jobs:
   regular_check:
-    runs-on: macos-latest
+    runs-on: macos-12
     if: github.event_name != 'schedule'
     steps:
       - name: Checkout
         uses: actions/checkout@main
       - name: Setup Python environment
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4.3.1
         with:
           python-version: '3.8'
       - name: Check without sanitizer
         uses: ./.github/actions/build_and_check
         with:
           asan: false
           ubsan: false
-          check_skip_long: false
 
   sanitizer_check:
-    runs-on: macos-latest
+    permissions:
+      contents: read # to fetch code (actions/checkout)
+      issues: write # to create an issue
+
+    runs-on: macos-12
     if: (github.event_name == 'schedule' && github.repository == 'espressomd/espresso')
     steps:
       - name: Checkout
         uses: actions/checkout@main
       - name: Setup Python environment
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4.3.1
         with:
           python-version: '3.8'
       - name: Check with sanitizer
         uses: ./.github/actions/build_and_check
         with:
           asan: true
           ubsan: true
-          check_skip_long: true
       - name: Setting job link variable
         if: ${{ failure() }}
         run: |

.gitlab-ci.yml

@@ -1,4 +1,4 @@
-image: ghcr.io/espressomd/docker/ubuntu-20.04:7ec021ab4af6f89d65121db2eb24acb1ed452e02
+image: ghcr.io/espressomd/docker/ubuntu-20.04:7db5674cf3eca1ce80a5ce970661494ec6612924
 
 stages:
   - prepare
@@ -136,7 +136,7 @@ no_rotation:
 ubuntu:wo-dependencies:
   <<: *global_job_definition
   stage: build
-  image: ghcr.io/espressomd/docker/ubuntu-wo-dependencies:7ec021ab4af6f89d65121db2eb24acb1ed452e02
+  image: ghcr.io/espressomd/docker/ubuntu-wo-dependencies:7db5674cf3eca1ce80a5ce970661494ec6612924
   variables:
      myconfig: 'maxset'
      with_cuda: 'false'
@@ -154,7 +154,7 @@ ubuntu:wo-dependencies:
 debian:10:
   <<: *global_job_definition
   stage: build
-  image: ghcr.io/espressomd/docker/debian:7ec021ab4af6f89d65121db2eb24acb1ed452e02
+  image: ghcr.io/espressomd/docker/debian:7db5674cf3eca1ce80a5ce970661494ec6612924
   variables:
      with_cuda: 'false'
      myconfig: 'maxset'
@@ -169,7 +169,7 @@ debian:10:
 fedora:36:
   <<: *global_job_definition
   stage: build
-  image: ghcr.io/espressomd/docker/fedora:7ec021ab4af6f89d65121db2eb24acb1ed452e02
+  image: ghcr.io/espressomd/docker/fedora:7db5674cf3eca1ce80a5ce970661494ec6612924
   variables:
      with_cuda: 'false'
      myconfig: 'maxset'
@@ -210,7 +210,7 @@ clang-sanitizer:
 fast_math:
   <<: *global_job_definition
   stage: build
-  image: ghcr.io/espressomd/docker/cuda:7ec021ab4af6f89d65121db2eb24acb1ed452e02
+  image: ghcr.io/espressomd/docker/cuda:7db5674cf3eca1ce80a5ce970661494ec6612924
   variables:
      CC: 'gcc-9'
      CXX: 'g++-9'
@@ -230,7 +230,7 @@ fast_math:
 cuda11-maxset-ubuntu20.04:
   <<: *global_job_definition
   stage: build
-  image: ghcr.io/espressomd/docker/cuda:7ec021ab4af6f89d65121db2eb24acb1ed452e02
+  image: ghcr.io/espressomd/docker/cuda:7db5674cf3eca1ce80a5ce970661494ec6612924
   variables:
      CC: 'gcc-9'
      CXX: 'g++-9'
@@ -251,7 +251,7 @@ cuda11-maxset-ubuntu20.04:
 cuda11-maxset-ubuntu22.04:
   <<: *global_job_definition
   stage: build
-  image: ghcr.io/espressomd/docker/ubuntu-22.04:7ec021ab4af6f89d65121db2eb24acb1ed452e02
+  image: ghcr.io/espressomd/docker/ubuntu-22.04:7db5674cf3eca1ce80a5ce970661494ec6612924
   variables:
      CC: 'gcc-10'
      CXX: 'g++-10'
@@ -305,6 +305,7 @@ tutorials-samples-maxset:
      with_coverage: 'false'
      with_coverage_python: 'true'
      with_scafacos: 'true'
+     with_stokesian_dynamics: 'true'
      make_check_unit_tests: 'false'
      make_check_python: 'false'
      make_check_tutorials: 'true'
@@ -438,6 +439,8 @@ 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:

CMakeLists.txt

@@ -96,6 +96,10 @@ if(CMAKE_CXX_COMPILER_ID MATCHES "Clang" AND NOT APPLE)
     "Build with memory sanitizer (experimental; requires a memory-sanitized Python interpreter)"
     OFF)
 endif()
+option(
+  ESPRESSO_ADD_OMPI_SINGLETON_WARNING
+  "Add a runtime warning in the pypresso script for NUMA architectures that aren't supported in singleton mode by Open MPI 4.x"
+  ON)
 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)
@@ -104,14 +108,13 @@ set(TEST_TIMEOUT "300" CACHE STRING
                              "Timeout in seconds for each testsuite test")
 
 if(WITH_CCACHE)
-  find_program(CCACHE ccache)
-  if(CCACHE)
-    message(STATUS "Found ccache ${CCACHE}")
-    set(CMAKE_CXX_COMPILER_LAUNCHER ${CCACHE} CACHE STRING "ccache executable")
-  else()
-    message(FATAL_ERROR "ccache not found.")
-  endif(CCACHE)
-endif(WITH_CCACHE)
+  find_program(CCACHE_PROGRAM ccache REQUIRED)
+  if(CCACHE_PROGRAM)
+    message(STATUS "Found ccache: ${CCACHE_PROGRAM}")
+    set(CMAKE_CXX_COMPILER_LAUNCHER ${CCACHE_PROGRAM})
+    set(CMAKE_CUDA_COMPILER_LAUNCHER ${CCACHE_PROGRAM})
+  endif()
+endif()
 
 # Write compile commands to file, for various tools...
 set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
@@ -280,11 +283,38 @@ 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 "")
+set(MPIEXEC_OVERSUBSCRIBE "")
+# Open MPI 4.x has a bug on NUMA archs that prevents running in singleton mode
+set(ESPRESSO_MPIEXEC_GUARD_SINGLETON_NUMA OFF)
+set(ESPRESSO_CPU_MODEL_NAME_OMPI_SINGLETON_NUMA_PATTERN "AMD (EPYC|Ryzen)")
+
+if("${MPIEXEC_BACKEND_NAME}" STREQUAL "OpenMPI")
+  if("${MPIEXEC_BACKEND_VERSION}" VERSION_GREATER_EQUAL 2.0.0)
+    set(MPIEXEC_OVERSUBSCRIBE "-oversubscribe")
+  endif()
+  if("${MPIEXEC_BACKEND_VERSION}" VERSION_GREATER_EQUAL 4.0
+     AND "${MPIEXEC_BACKEND_VERSION}" VERSION_LESS 5.0)
+    if(NOT DEFINED ESPRESSO_CPU_MODEL_NAME)
+      if(CMAKE_SYSTEM_NAME STREQUAL Linux)
+        if(EXISTS /proc/cpuinfo)
+          file(READ /proc/cpuinfo ESPRESSO_CPU_INFO)
+          string(REGEX
+                 REPLACE ".*\n[Mm]odel name[ \t]*:[ \t]+([^\n]+).*" "\\1"
+                         ESPRESSO_CPU_MODEL_NAME_STRING "${ESPRESSO_CPU_INFO}")
+        else()
+          set(ESPRESSO_CPU_MODEL_NAME_STRING "__unreadable")
+        endif()
+      else()
+        set(ESPRESSO_CPU_MODEL_NAME_STRING "__unaffected")
+      endif()
+      set(ESPRESSO_CPU_MODEL_NAME "${ESPRESSO_CPU_MODEL_NAME_STRING}"
+          CACHE INTERNAL "")
+    endif()
+    if(ESPRESSO_CPU_MODEL_NAME MATCHES
+       "^${ESPRESSO_CPU_MODEL_NAME_OMPI_SINGLETON_NUMA_PATTERN}")
+      set(ESPRESSO_MPIEXEC_GUARD_SINGLETON_NUMA ON)
+    endif()
+  endif()
 endif()
 
 # OpenMPI cannot run two jobs in parallel in a Docker container, because the

cmake/FindCUDACompilerClang.cmake

@@ -62,8 +62,25 @@ set(CUDA_NVCC_FLAGS_RELWITHASSERT "${CUDA_NVCC_FLAGS_RELWITHASSERT} -O3 -g")
 string(TOUPPER ${CMAKE_BUILD_TYPE} CMAKE_BUILD_TYPE_UPPER)
 set(gpu_interface_flags "${CUDA_NVCC_FLAGS} ${CUDA_NVCC_FLAGS_${CMAKE_BUILD_TYPE_UPPER}} --cuda-gpu-arch=sm_52")
 if(CMAKE_CUDA_COMPILER_VERSION VERSION_LESS 11)
+  # GTX-600 series (Kepler)
   set(gpu_interface_flags "${gpu_interface_flags} --cuda-gpu-arch=sm_30")
 endif()
+if(CMAKE_CUDA_COMPILER_VERSION VERSION_LESS 12)
+  # GTX-900 series (Maxwell)
+  set(gpu_interface_flags "${gpu_interface_flags} --cuda-gpu-arch=sm_52")
+endif()
+if(CMAKE_CUDA_COMPILER_VERSION VERSION_GREATER_EQUAL 10)
+  # GTX-1000 series (Pascal)
+  set(gpu_interface_flags "${gpu_interface_flags} --cuda-gpu-arch=sm_61")
+endif()
+if(CMAKE_CUDA_COMPILER_VERSION VERSION_GREATER_EQUAL "10.0.0" AND
+   (CMAKE_CUDA_COMPILER_VERSION VERSION_LESS "14.0.0" OR
+   CUDA_VERSION VERSION_GREATER_EQUAL "11.3.0"))
+  # RTX-2000 series (Turing)
+  # With Clang 14+, architectures sm_70+ are only supported with Thrust 1.11+
+  # from CUDA 11.3+, for details see https://github.com/NVIDIA/cub/pull/170
+  set(gpu_interface_flags "${gpu_interface_flags} --cuda-gpu-arch=sm_75")
+endif()
 if(CMAKE_CUDA_COMPILER_VERSION VERSION_GREATER_EQUAL "12.0.0" AND
    CMAKE_CUDA_COMPILER_VERSION VERSION_LESS "13.0.0" AND
    CUDA_VERSION VERSION_GREATER_EQUAL "11.0" AND

cmake/FindCUDACompilerNVCC.cmake

@@ -77,7 +77,7 @@ find_gpu_library(VARNAME CUDA_CUFFT_LIBRARIES NAMES cufft REQUIRED)
 function(add_gpu_library)
   cuda_add_library(${ARGV})
   set(GPU_TARGET_NAME ${ARGV0})
-  set_property(TARGET ${GPU_TARGET_NAME} PROPERTY CUDA_SEPARABLE_COMPILATION ON)
+  set_target_properties(${GPU_TARGET_NAME} PROPERTIES CUDA_SEPARABLE_COMPILATION ON)
   target_link_libraries(${GPU_TARGET_NAME} PRIVATE
     ${CUDA_LIBRARY} ${CUDART_LIBRARY} ${CUDA_CUFFT_LIBRARIES})
 endfunction()

cmake/FindClangTidy.cmake

@@ -1,3 +1,22 @@
+#
+# Copyright (C) 2017-2022 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 Clang-tidy
 
 # get Clang version

cmake/FindSphinx.cmake

@@ -1,3 +1,22 @@
+#
+# Copyright (C) 2016-2022 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/>.
+#
+
 include(FindPackageHandleStandardArgs)
 
 set(SPHINX_EXECUTABLE ${PYTHON_EXECUTABLE} -m sphinx)

cmake/cmake_config.cmakein

@@ -3,8 +3,6 @@
 
 #cmakedefine CUDA
 
-#cmakedefine HIP
-
 #cmakedefine FFTW
 
 #cmakedefine H5MD
@@ -13,10 +11,6 @@
 
 #cmakedefine GSL
 
-#cmakedefine BLAS
-
-#cmakedefine LAPACK
-
 #cmakedefine STOKESIAN_DYNAMICS
 
 #cmakedefine VALGRIND_INSTRUMENTATION