diff --git a/.clang-tidy b/.clang-tidy
index a996e64c0a..8d269d52fa 100644
--- a/.clang-tidy
+++ b/.clang-tidy
@@ -10,6 +10,8 @@ Checks: |
-bugprone-implicit-widening-of-multiplication-result,
-bugprone-macro-parentheses,
-bugprone-reserved-identifier,
+ -bugprone-switch-missing-default-case,
+ -bugprone-unchecked-optional-access,
clang-analyzer-alpha.*,
modernize-deprecated-headers,
modernize-make-shared,
@@ -41,7 +43,6 @@ Checks: |
readability-function-size'
WarningsAsErrors: '*,-clang-analyzer-core.StackAddrEscapeBase,-clang-analyzer-optin.mpi.MPI-Checker'
HeaderFilterRegex: '.*'
-AnalyzeTemporaryDtors: false
FormatStyle: none
User: espresso
CheckOptions:
diff --git a/.github/actions/build_and_check/action.yml b/.github/actions/build_and_check/action.yml
index 6a4e4d6e71..0e9546d98b 100644
--- a/.github/actions/build_and_check/action.yml
+++ b/.github/actions/build_and_check/action.yml
@@ -1,24 +1,15 @@
name: 'Build and check'
-description: 'Build espresso and run checks'
-inputs:
- asan: # id of input
- description: 'Whether to build with address sanitizer'
- required: true
- default: 'false'
- ubsan:
- description: 'Whether to build with undefined behavior sanitizer'
- required: true
- default: 'false'
+description: 'Build ESPResSo and run checks'
runs:
using: "composite"
steps:
- run: |
brew install boost boost-mpi fftw
brew install hdf5-mpi
- pip3 install -c requirements.txt numpy cython h5py scipy
+ pip3 install -c requirements.txt "cython<3.0" numpy scipy h5py packaging
shell: bash
- run: |
- export myconfig=maxset with_cuda=false test_timeout=800 with_asan=${{ inputs.asan }} with_ubsan=${{ inputs.ubsan }} check_skip_long=true
+ export myconfig=maxset with_cuda=false with_gsl=false test_timeout=800 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
diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml
index 06de904ae7..7ab35c52b7 100644
--- a/.github/workflows/deploy.yml
+++ b/.github/workflows/deploy.yml
@@ -16,7 +16,7 @@ jobs:
- name: Install pandoc
uses: r-lib/actions/setup-pandoc@v2
- name: Setup SSH agent
- uses: webfactory/ssh-agent@v0.7.0
+ uses: webfactory/ssh-agent@v0.9.0
with:
ssh-private-key: ${{ secrets.GH_PAGES_SSH_PRIVATE_KEY }}
- name: Checkout
diff --git a/.github/workflows/push_pull.yml b/.github/workflows/push_pull.yml
index 82229ac665..b16c9752e0 100644
--- a/.github/workflows/push_pull.yml
+++ b/.github/workflows/push_pull.yml
@@ -1,57 +1,24 @@
-name: run tests on mac
+name: run tests on macOS
on:
push:
pull_request:
- schedule:
- - cron: '0 3 * * *'
permissions:
contents: read # to fetch code (actions/checkout)
jobs:
- regular_check:
- runs-on: macos-12
- if: github.event_name != 'schedule'
+ macos:
+ runs-on: macos-13
steps:
- name: Checkout
uses: actions/checkout@main
- name: Setup Python environment
- uses: actions/setup-python@v4.3.1
+ uses: actions/setup-python@v5.1.0
with:
- python-version: '3.8'
- - name: Check without sanitizer
+ python-version: '3.9'
+ - name: Build and check
uses: ./.github/actions/build_and_check
- with:
- asan: false
- ubsan: false
-
- sanitizer_check:
- 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@v4.3.1
- with:
- python-version: '3.8'
- - name: Check with sanitizer
- uses: ./.github/actions/build_and_check
- with:
- asan: true
- ubsan: true
- - name: Setting job link variable
- if: ${{ failure() }}
- run: |
- echo "job_link=${GITHUB_SERVER_URL}/${GITHUB_REPOSITORY}/actions/runs/${GITHUB_RUN_ID}" >> $GITHUB_ENV
- - uses: alialaa/issue-action@v1
- if: ${{ failure() }}
- with:
- token: ${{ secrets.GITHUB_TOKEN }}
- title: Scheduled CI job has failed
- body: ${{ env.job_link }}
+ env:
+ build_procs: 4
+ check_procs: 4
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 83f4866e6d..873d6e86be 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -166,6 +166,21 @@ debian:10:
- espresso
- no-cuda
+debian:12:
+ <<: *global_job_definition
+ stage: build
+ image: ghcr.io/espressomd/docker/debian:f7f8ef2c0ca93c67aa16b9f91785492fb04ecc1b
+ variables:
+ with_cuda: 'false'
+ myconfig: 'maxset'
+ make_check_python: 'false'
+ with_stokesian_dynamics: 'true'
+ script:
+ - bash maintainer/CI/build_cmake.sh
+ tags:
+ - espresso
+ - no-cuda
+
fedora:36:
<<: *global_job_definition
stage: build
@@ -181,6 +196,23 @@ fedora:36:
- espresso
- no-cuda
+fedora:40:
+ <<: *global_job_definition
+ stage: build
+ image: ghcr.io/espressomd/docker/fedora:f7f8ef2c0ca93c67aa16b9f91785492fb04ecc1b
+ variables:
+ with_cuda: 'false'
+ with_gsl: 'false'
+ myconfig: 'maxset'
+ make_check_python: 'true'
+ with_stokesian_dynamics: 'true'
+ cmake_params: '-D CMAKE_INCLUDE_PATH=/usr/include/mpich-x86_64 -D CMAKE_PREFIX_PATH=/usr/lib64/mpich/lib/'
+ script:
+ - bash maintainer/CI/build_cmake.sh
+ tags:
+ - espresso
+ - no-cuda
+
### Builds with CUDA
clang-sanitizer:
@@ -227,6 +259,28 @@ fast_math:
- cuda
when: manual
+cuda12-maxset-ubuntu24.04:
+ <<: *global_job_definition
+ stage: build
+ image: ghcr.io/espressomd/docker/ubuntu:f7f8ef2c0ca93c67aa16b9f91785492fb04ecc1b
+ variables:
+ CC: 'gcc-12'
+ CXX: 'g++-12'
+ GCOV: 'gcov-12'
+ myconfig: 'maxset'
+ with_cuda: 'true'
+ with_coverage: 'false'
+ with_coverage_python: 'false'
+ check_skip_long: 'false'
+ with_scafacos: 'true'
+ with_stokesian_dynamics: 'true'
+ script:
+ - bash maintainer/CI/build_cmake.sh
+ tags:
+ - espresso
+ - cuda
+ - numa
+
cuda11-maxset-ubuntu20.04:
<<: *global_job_definition
stage: build
@@ -238,6 +292,7 @@ cuda11-maxset-ubuntu20.04:
myconfig: 'maxset'
with_cuda: 'true'
with_coverage: 'true'
+ with_coverage_python: 'true'
check_skip_long: 'true'
with_scafacos: 'true'
with_stokesian_dynamics: 'true'
@@ -259,6 +314,7 @@ cuda11-maxset-ubuntu22.04:
myconfig: 'maxset'
with_cuda: 'true'
with_coverage: 'true'
+ with_coverage_python: 'true'
check_skip_long: 'true'
with_scafacos: 'true'
with_stokesian_dynamics: 'true'
@@ -489,6 +545,7 @@ run_tutorials:
paths:
- build/doc/tutorials
expire_in: 1 week
+ timeout: 2h
tags:
- espresso
- cuda
diff --git a/doc/sphinx/installation.rst b/doc/sphinx/installation.rst
index f4ff1d6850..a7e3bc84b6 100644
--- a/doc/sphinx/installation.rst
+++ b/doc/sphinx/installation.rst
@@ -25,7 +25,7 @@ performance of the code. Therefore it is not possible to build a single
binary that can satisfy all needs. For performance reasons a user
should always activate only those features that are actually needed.
This means, however, that learning how to compile is a necessary evil.
-The build system of |es| uses CMake [4]_ to compile
+The build system of |es| uses CMake to compile
software easily on a wide range of platforms.
.. _Requirements:
@@ -39,7 +39,7 @@ are required to be able to compile and use |es|:
.. glossary::
CMake
- The build system is based on CMake.
+ The build system is based on CMake version 3 or later [4]_.
C++ compiler
The C++ core of |es| needs to be built by a C++14-capable compiler.
@@ -52,6 +52,11 @@ are required to be able to compile and use |es|:
For some algorithms like P\ :math:`^3`\ M, |es| needs the FFTW library
version 3 or later [5]_ for Fourier transforms, including header files.
+ CUDA
+ For some algorithms like P\ :math:`^3`\ M,
+ |es| provides GPU-accelerated implementations for NVIDIA GPUs.
+ We strongly recommend CUDA 12.0 or later [6]_.
+
MPI
An MPI library that implements the MPI standard version 1.2 is required
to run simulations in parallel. |es| is currently tested against
@@ -247,11 +252,11 @@ Installing requirements on Windows via WSL
To run |es| on Windows, use the Linux subsystem. For that you need to
-* follow `these instructions <https://docs.microsoft.com/en-us/windows/wsl/install-win10>`__ to install Ubuntu
-* start Ubuntu (or open an Ubuntu tab in `Windows Terminal <https://www.microsoft.com/en-us/p/windows-terminal/9n0dx20hk701>`__)
+* follow `these instructions <https://learn.microsoft.com/en-us/windows/wsl/install>`__ to install Ubuntu
+* start Ubuntu (or open an Ubuntu tab in `Windows Terminal <https://apps.microsoft.com/detail/9n0dx20hk701?hl=en-us&gl=US>`__)
* execute ``sudo apt update`` to prepare the installation of dependencies
* optional step: If you have a NVIDIA graphics card available and want to make
- use of |es|'s GPU acceleration, follow `these instructions <https://docs.nvidia.com/cuda/wsl-user-guide/index.html#ch03a-setting-up-cuda>`__
+ use of |es|'s GPU acceleration, follow `these instructions <https://docs.nvidia.com/cuda/wsl-user-guide/index.html>`__
to set up CUDA.
* follow the instructions for :ref:`Installing requirements on Ubuntu Linux`
diff --git a/doc/tutorials/error_analysis/error_analysis_part2.ipynb b/doc/tutorials/error_analysis/error_analysis_part2.ipynb
index 29c64d029c..cbce23701c 100644
--- a/doc/tutorials/error_analysis/error_analysis_part2.ipynb
+++ b/doc/tutorials/error_analysis/error_analysis_part2.ipynb
@@ -205,7 +205,8 @@
"plt.plot(autocov)\n",
"plt.xlabel(\"lag time $j$\")\n",
"plt.ylabel(r\"$\\hat{K}^{XX}_j$\")\n",
- "plt.show()"
+ "plt.show()\n",
+ "```"
]
},
{
diff --git a/src/config/config.hpp b/src/config/config.hpp
index 0363426466..02a74e38ad 100644
--- a/src/config/config.hpp
+++ b/src/config/config.hpp
@@ -54,7 +54,7 @@
#endif
/** Whether to use the approximation of Abramowitz/Stegun @cite abramowitz65a
- * @ref AS_erfc_part() for \f$\exp(d^2) \mathrm{erfc}(d)\f$,
+ * @ref Utils::AS_erfc_part() for \f$\exp(d^2) \mathrm{erfc}(d)\f$,
* or the C function <tt>std::erfc()</tt> in P3M and Ewald summation.
*/
#ifndef USE_ERFC_APPROXIMATION
diff --git a/src/core/statistics.cpp b/src/core/statistics.cpp
index 0dd94319fe..c11f087f3d 100644
--- a/src/core/statistics.cpp
+++ b/src/core/statistics.cpp
@@ -133,18 +133,15 @@ Utils::Vector3d angularmomentum(PartCfg &partCfg, int type) {
}
void momentofinertiamatrix(PartCfg &partCfg, int type, double *MofImatrix) {
- int i, count;
double massi;
Utils::Vector3d p1{};
- count = 0;
- for (i = 0; i < 9; i++)
+ for (unsigned int i = 0; i < 9; i++)
MofImatrix[i] = 0.;
auto const com = centerofmass(partCfg, type);
for (auto const &p : partCfg) {
if (type == p.type() and (not p.is_virtual())) {
- count++;
p1 = p.pos() - com;
massi = p.mass();
MofImatrix[0] += massi * (p1[1] * p1[1] + p1[2] * p1[2]);
diff --git a/src/python/espressomd/CMakeLists.txt b/src/python/espressomd/CMakeLists.txt
index 2a18f5f6ca..a508e799e3 100644
--- a/src/python/espressomd/CMakeLists.txt
+++ b/src/python/espressomd/CMakeLists.txt
@@ -73,6 +73,10 @@ elseif(CMAKE_CXX_COMPILER_ID STREQUAL "Clang" OR CMAKE_CXX_COMPILER_ID STREQUAL
Espresso_pyx_flags
INTERFACE -Wno-pedantic -Wno-\#warnings -Wno-sometimes-uninitialized
-Wno-unused-variable -Wno-deprecated-declarations)
+ if(CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang")
+ target_compile_options(Espresso_pyx_flags
+ INTERFACE -Wno-missing-field-initializers)
+ endif()
elseif(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
target_compile_options(Espresso_pyx_flags INTERFACE -wd1224)
else()
@@ -105,10 +109,9 @@ foreach(cython_file ${cython_SRC})
add_custom_command(
OUTPUT ${outputpath}
COMMAND
- ${CYTHON_EXECUTABLE} $<$<BOOL:${WARNINGS_ARE_ERRORS}>:--warning-errors>
- -3 --cplus --directive embedsignature=True --directive binding=True -I
- ${CMAKE_CURRENT_SOURCE_DIR} -I ${CMAKE_CURRENT_BINARY_DIR}
- ${cython_file} -o ${outputpath}
+ ${CYTHON_EXECUTABLE} -3 --cplus --directive embedsignature=True
+ --directive binding=True -I ${CMAKE_CURRENT_SOURCE_DIR} -I
+ ${CMAKE_CURRENT_BINARY_DIR} ${cython_file} -o ${outputpath}
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/..
DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/myconfig.pxi ${cython_file}
${cython_HEADER})
diff --git a/testsuite/python/sigint_child.py b/testsuite/python/sigint_child.py
index ed86ecec3c..efd63e36b7 100644
--- a/testsuite/python/sigint_child.py
+++ b/testsuite/python/sigint_child.py
@@ -19,6 +19,8 @@
import numpy as np
import espressomd
+np.random.seed(42)
+
system = espressomd.System(box_l=[100, 100, 100])
system.time_step = 0.01
system.cell_system.skin = 0.1