2. Installation

This chapter will describe how to get, compile and run the software.

ESPResSo releases are available as source code packages from the homepage 1. This is where new users should get the code. The code within release packages is tested and known to run on a number of platforms. Alternatively, people that want to use the newest features of ESPResSo or that want to start contributing to the software can instead obtain the current development code via the version control system software 2 from ESPResSo’s project page at Github 3. This code might be not as well tested and documented as the release code; it is recommended to use this code only if you have already gained some experience in using ESPResSo.

Unlike most other software, no binary distributions of ESPResSo are available, and the software is usually not installed globally for all users. Instead, users of ESPResSo should compile the software themselves. The reason for this is that it is possible to activate and deactivate various features before compiling the code. Some of these features are not compatible with each other, and some of the features have a profound impact on the 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 ESPResSo uses CMake 4 to compile software easily on a wide range of platforms.

2.1. Requirements

The following tools and libraries, including their header files, are required to be able to compile and use ESPResSo:

CMake

The build system is based on CMake.

C++ compiler

The C++ core of ESPResSo needs to be built by a C++14-capable compiler.

Boost

A number of advanced C++ features used by ESPResSo are provided by Boost. We strongly recommend to use at least Boost 1.71.

FFTW

For some algorithms like P\(^3\)M, ESPResSo needs the FFTW library version 3 or later 5 for Fourier transforms, including header files.

MPI

An MPI library that implements the MPI standard version 1.2 is required to run simulations in parallel. ESPResSo is currently tested against Open MPI and MPICH, with and without UCX enabled. Other MPI implementations like Intel MPI should also work, although they are not actively tested in ESPResSo continuous integration.

Python

ESPResSo’s main user interface relies on Python 3.

Cython

Cython is used for connecting the C++ core to Python.

2.1.1. Installing requirements on Ubuntu Linux

To compile ESPResSo on Ubuntu 22.04 LTS, install the following dependencies:

sudo apt install build-essential cmake cython3 python3-pip python3-numpy \
  libboost-all-dev openmpi-common fftw3-dev libhdf5-dev libhdf5-openmpi-dev \
  python3-scipy python3-opengl libgsl-dev

Optionally the ccmake utility can be installed for easier configuration:

sudo apt install cmake-curses-gui

2.1.1.1. Nvidia GPU acceleration

If your computer has an Nvidia graphics card, you should also download and install the CUDA SDK to make use of GPU computation:

sudo apt install nvidia-cuda-toolkit

On Ubuntu 22.04, the default GCC compiler is too recent for nvcc and will fail to compile sources that rely on std::function. You can either use GCC 10:

CC=gcc-10 CXX=g++-10 cmake .. -D WITH_CUDA=ON
make -j

or alternatively install Clang 12 as a replacement for nvcc and GCC:

CC=clang-12 CXX=clang++-12 cmake .. -D WITH_CUDA=ON -D WITH_CUDA_COMPILER=clang
make -j

On Ubuntu 20.04, the default GCC compiler is also too recent for nvcc and will generate compiler errors. You can either install an older version of GCC and select it with environment variables CC and CXX when building ESPResSo, or edit the system header files as shown in the following patch for Ubuntu 20.04.

2.1.1.2. Requirements for building the documentation

To generate the Sphinx documentation, install the following packages:

pip3 install --user \
    'sphinx>=2.3.0,!=3.0.0' \
    'sphinxcontrib-bibtex>=2.4.1' \
    'sphinx-toggleprompt==0.0.5'

To generate the Doxygen documentation, install the following packages:

sudo apt install doxygen graphviz

2.1.1.3. Setting up a Jupyter environment

To run the samples and tutorials, start by installing the following packages:

sudo apt install python3-matplotlib python3-pint python3-tqdm ffmpeg
pip3 install --user 'MDAnalysis>=1.0.0,<2.0.0'

The tutorials are written in the Notebook Format version <= 4.4 and can be executed by any of these tools:

To check whether one of them is installed, run these commands:

jupyter notebook --version
jupyter lab --version
ipython --version

If you don’t have any of these tools installed and aren’t sure which one to use, we recommend installing the historic Jupyter Notebook, since the ESPResSo tutorials have been designed with the exercise2 plugin in mind.

To use Jupyter Notebook, install the following packages:

pip3 install --user nbformat notebook 'jupyter_contrib_nbextensions==0.5.1'
jupyter contrib nbextension install --user
jupyter nbextension enable rubberband/main
jupyter nbextension enable exercise2/main

Alternatively, to use JupyterLab, install the following packages:

pip3 install --user nbformat notebook jupyterlab

2.1.2. Installing requirements on other Linux distributions

Please refer to the following Dockerfiles to find the minimum set of packages required to compile ESPResSo on other Linux distributions:

2.1.3. Installing requirements on Windows via WSL

To run ESPResSo on Windows, use the Linux subsystem. For that you need to

2.1.4. Installing requirements on macOS

To build ESPResSo on macOS 10.15 or higher, you need to install its dependencies. There are two possibilities for this, MacPorts and Homebrew. We strongly recommend Homebrew, but if you already have MacPorts installed, you can use that too, although we do not provide MacPorts installation instructions.

To check whether you already have one or the other installed, run the following commands:

test -e /opt/local/bin/port && echo "MacPorts is installed"
test -e /usr/local/bin/brew && echo "Homebrew is installed"

If Homebrew is already installed, you should resolve any problems reported by the command

brew doctor

If you want to install Homebrew, follow the installation instructions at https://docs.brew.sh/Installation, but bear in mind that MacPorts and Homebrew may conflict with one another.

If Anaconda Python or the Python from www.python.org are installed, you will likely not be able to run ESPResSo. Therefore, please uninstall them using the following commands:

sudo rm -r ~/anaconda[23]
sudo rm -r /Library/Python

2.1.4.1. Installing packages using Homebrew

Run the following commands:

brew install cmake python cython boost boost-mpi fftw \
  doxygen gsl numpy scipy ipython jupyter
brew install hdf5-mpi
brew link --force cython
pip install PyOpenGL matplotlib

2.2. Quick installation

If you have installed the requirements (see section Requirements) in standard locations, compiling ESPResSo is usually only a matter of creating a build directory and calling cmake and make in it. See for example the command lines below (optional steps which modify the build process are commented out):

mkdir build
cd build
cmake ..
#ccmake . // in order to add/remove features like ScaFaCoS or CUDA
make -j

This will build ESPResSo with a default feature set, namely src/config/myconfig-default.hpp. This file is a C++ header file, which defines the features that should be compiled in. You may want to adjust the feature set to your needs. This can be easily done by copying the myconfig-sample.hpp which has been created in the build directory to myconfig.hpp and only uncomment the features you want to use in your simulation.

The cmake command looks for libraries and tools needed by ESPResSo. So ESPResSo can only be built if cmake reports no errors.

The command make will compile the source code. Depending on the options passed to the program, make can also be used for a number of other things:

  • It can install and uninstall the program to some other directories. However, normally it is not necessary to actually install to run it: make install

  • It can invoke code checks: make check

  • It can build this documentation: make sphinx

When these steps have successfully completed, ESPResSo can be started with the command:

./pypresso script.py

where script.py is a Python script which has to be written by the user. You can find some examples in the samples folder of the source code directory. If you want to run in parallel, you should have compiled with an MPI library, and need to tell MPI to run in parallel. The actual invocation is implementation-dependent, but in many cases, such as Open MPI and MPICH, you can use

mpirun -n 4 ./pypresso script.py

where 4 is the number of processors to be used.

2.3. Features

This chapter describes the features that can be activated in ESPResSo. Even if possible, it is not recommended to activate all features, because this will negatively affect ESPResSo’s performance.

Features can be activated in the configuration header myconfig.hpp (see section myconfig.hpp: Activating and deactivating features). To activate FEATURE, add the following line to the header file:

#define FEATURE

2.3.1. General features

  • ELECTROSTATICS This enables the use of the various electrostatics algorithms, such as P3M.

    See also

    Electrostatics

  • MMM1D_GPU: This enables MMM1D on GPU. It is faster than the CPU version by several orders of magnitude, but has float precision instead of double precision.

  • MMM1D_MACHINE_PREC: This enables high-precision Bessel functions for MMM1D on CPU. Comes with a 60% slow-down penalty. The low-precision functions are enabled by default and are precise enough for most applications.

  • DIPOLES This activates the dipole-moment property of particles and switches on various magnetostatics algorithms

    See also

    Magnetostatics

  • SCAFACOS_DIPOLES This activates magnetostatics methods of ScaFaCoS.

  • DIPOLAR_DIRECT_SUM This activates the GPU implementation of the dipolar direct sum.

  • ROTATION Switch on rotational degrees of freedom for the particles, as well as the corresponding quaternion integrator.

    See also

    Setting up particles

    Note

    When this feature is activated, every particle has three additional degrees of freedom, which for example means that the kinetic energy changes at constant temperature is twice as large.

  • THERMOSTAT_PER_PARTICLE Allows setting a per-particle friction coefficient for the Langevin and Brownian thermostats.

  • ROTATIONAL_INERTIA

  • EXTERNAL_FORCES Allows to define an arbitrary constant force for each particle individually. Also allows to fix individual coordinates of particles, keep them at a fixed position or within a plane.

  • MASS Allows particles to have individual masses. Note that some analysis procedures have not yet been adapted to take the masses into account correctly.

    See also

    espressomd.particle_data.ParticleHandle.mass

  • EXCLUSIONS Allows to exclude specific short ranged interactions within molecules.

    See also

    espressomd.particle_data.ParticleHandle.add_exclusion()

  • BOND_CONSTRAINT Turns on the RATTLE integrator which allows for fixed lengths bonds between particles.

  • VIRTUAL_SITES_RELATIVE Virtual sites are particles, the position and velocity of which is not obtained by integrating equations of motion. Rather, they are placed using the position (and orientation) of other particles. The feature allows for rigid arrangements of particles.

    See also

    Virtual sites

  • COLLISION_DETECTION Allows particles to be bound on collision.

In addition, there are switches that enable additional features in the integrator or thermostat:

2.3.2. Fluid dynamics and fluid structure interaction

  • DPD Enables the dissipative particle dynamics thermostat and interaction.

    See also

    DPD interaction

  • LB_BOUNDARIES

  • LB_BOUNDARIES_GPU

  • LB_ELECTROHYDRODYNAMICS Enables the implicit calculation of electro-hydrodynamics for charged particles and salt ions in an electric field.

  • ELECTROKINETICS

  • EK_BOUNDARIES

  • EK_DEBUG

2.3.3. Interaction features

The following switches turn on various short ranged interactions (see section Isotropic non-bonded interactions):

  • TABULATED Enable support for user-defined non-bonded interaction potentials.

  • LENNARD_JONES Enable the Lennard-Jones potential.

  • LENNARD_JONES_GENERIC Enable the generic Lennard-Jones potential with configurable exponents and individual prefactors for the two terms.

  • LJCOS Enable the Lennard-Jones potential with a cosine-tail.

  • LJCOS2 Same as LJCOS, but using a slightly different way of smoothing the connection to 0.

  • WCA Enable the Weeks–Chandler–Andersen potential.

  • GAY_BERNE Enable the Gay–Berne potential.

  • HERTZIAN Enable the Hertzian potential.

  • MORSE Enable the Morse potential.

  • BUCKINGHAM Enable the Buckingham potential.

  • SOFT_SPHERE Enable the soft sphere potential.

  • SMOOTH_STEP Enable the smooth step potential, a step potential with two length scales.

  • BMHTF_NACL Enable the Born–Meyer–Huggins–Tosi–Fumi potential, which can be used to model salt melts.

  • GAUSSIAN Enable the Gaussian potential.

  • HAT Enable the Hat potential.

Some of the short-range interactions have additional features:

  • LJGEN_SOFTCORE This modifies the generic Lennard-Jones potential (LENNARD_JONES_GENERIC) with tunable parameters.

  • THOLE See Thole correction

2.3.4. Debug messages

Finally, there is a flag for debugging:

  • ADDITIONAL_CHECKS Enables numerous additional checks which can detect inconsistencies especially in the cell systems. These checks are however too slow to be enabled in production runs.

    Note

    Because of a bug in OpenMPI versions 2.0-2.1, 3.0.0-3.0.2 and 3.1.0-3.1.2 that causes a segmentation fault when running the ESPResSo OpenGL visualizer with feature ADDITIONAL_CHECKS enabled together with either ELECTROSTATICS or DIPOLES, the subset of additional checks for those two features are disabled if an unpatched version of OpenMPI is detected during compilation.

2.3.5. External features

External features cannot be added to the myconfig.hpp file by the user. They are added by CMake if the corresponding dependency was found on the system. Some of these external features are optional and must be activated using a CMake flag (see Options and Variables).

2.4. Configuring

2.4.1. myconfig.hpp: Activating and deactivating features

ESPResSo has a large number of features that can be compiled into the binary. However, it is not recommended to actually compile in all possible features, as this will slow down ESPResSo significantly. Instead, compile in only the features that are actually required. A strong gain in speed can be achieved by disabling all non-bonded interactions except for a single one, e.g. LENNARD_JONES. For developers, it is also possible to turn on or off a number of debugging messages. The features and debug messages can be controlled via a configuration header file that contains C-preprocessor declarations. Subsection Features describes all available features. If a file named myconfig.hpp is present in the build directory when cmake is run, all features defined in it will be compiled in. If no such file exists, the configuration file src/config/myconfig-default.hpp will be used instead, which turns on the default features.

When you distinguish between the build and the source directory, the configuration header can be put in either of these. Note, however, that when a configuration header is found in both directories, the one in the build directory will be used.

By default, the configuration header is called myconfig.hpp. The configuration header can be used to compile different binary versions of with a different set of features from the same source directory. Suppose that you have a source directory $srcdir and two build directories $builddir1 and $builddir2 that contain different configuration headers:

  • $builddir1/myconfig.hpp:

    #define ELECTROSTATICS
#define LENNARD_JONES

  • $builddir2/myconfig.hpp:

    #define LJCOS

Then you can simply compile two different versions of ESPResSo via:

cd $builddir1
cmake ..
make

cd $builddir2
cmake ..
make

To see what features were activated in myconfig.hpp, run:

./pypresso

and then in the Python interpreter:

import espressomd
print(espressomd.features())

2.4.2. cmake

In order to build the first step is to create a build directory in which cmake can be executed. In cmake, the source directory (that contains all the source files) is completely separated from the build directory (where the files created by the build process are put). cmake is designed to not be executed in the source directory. cmake will determine how to use and where to find the compiler, as well as the different libraries and tools required by the compilation process. By having multiple build directories you can build several variants of ESPResSo, each variant having different activated features, and for as many platforms as you want.

Once you’ve run ccmake, you can list the configured variables with cmake -LAH -N . | less (uses a pager) or with ccmake .. and pressing key t to toggle the advanced mode on (uses the curses interface).

Example:

When the source directory is srcdir (the files where unpacked to this directory), then the user can create a build directory build below that path by calling mkdir srcdir/build. In the build directory cmake is to be executed, followed by a call to make. None of the files in the source directory are ever modified by the build process.

cd build
cmake ..
make -j

Afterwards ESPResSo can be run by calling ./pypresso from the command line.

2.4.3. ccmake

Optionally and for easier use, the curses interface to cmake can be used to configure ESPResSo interactively.

Example:

Alternatively to the previous example, instead of cmake, the ccmake executable is called in the build directory to configure ESPResSo, followed by a call to make:

cd build
ccmake ..
make

Fig. ccmake interface shows the interactive ccmake UI.

ccmake interface

ccmake interface

2.4.4. Options and Variables

The behavior of ESPResSo can be controlled by means of options and variables in the CMakeLists.txt file. Also options are defined there. The following options are available:

  • WITH_CUDA: Build with GPU support

  • WITH_HDF5: Build with HDF5

  • WITH_TESTS: Enable tests

  • WITH_SCAFACOS: Build with ScaFaCoS support

  • WITH_STOKESIAN_DYNAMICS Build with Stokesian Dynamics support

  • WITH_VALGRIND_INSTRUMENTATION: Build with valgrind instrumentation markers

When the value in the CMakeLists.txt file is set to ON, the corresponding option is created; if the value of the option is set to OFF, the corresponding option is not created. These options can also be modified by calling cmake with the command line argument -D:

cmake -D WITH_HDF5=OFF ..

When an option is activated, additional options may become available. For example with -D WITH_CUDA=ON, one can choose the CUDA compiler with -D WITH_CUDA_COMPILER=<compiler_id>, where <compiler_id> can be nvcc (default) or clang.

Environment variables can be passed to CMake. For example, to select Clang, use CC=clang CXX=clang++ cmake .. -DWITH_CUDA=ON -DWITH_CUDA_COMPILER=clang. If you have multiple versions of the CUDA library installed, you can select the correct one with CUDA_BIN_PATH=/usr/local/cuda-10.0 cmake .. -DWITH_CUDA=ON (with Clang as the CUDA compiler, you also need to override its default CUDA path with -DCMAKE_CXX_FLAGS=--cuda-path=/usr/local/cuda-10.0).

2.4.4.1. Build types and compiler flags

The build type is controlled by -D CMAKE_BUILD_TYPE=<type> where <type> can take one of the following values:

  • Release: for production use: disables assertions and debug information, enables -O3 optimization (this is the default)

  • RelWithAssert: for debugging purposes: enables assertions and -O3 optimization (use this to track the source of a fatal error)

  • Debug: for debugging in GDB

  • Coverage: for code coverage

Cluster users and HPC developers may be interested in manually editing the Espresso_cpp_flags target in the top-level CMakeLists.txt file for finer control over compiler flags. The variable declaration is followed by a series of conditionals to enable or disable compiler-specific flags. Compiler flags passed to CMake via the -DCMAKE_CXX_FLAGS option (such as cmake . -DCMAKE_CXX_FLAGS="-ffast-math -fno-finite-math-only") will appear in the compiler command before the flags in Espresso_cpp_flags, and will therefore have lower precedence.

Be aware that fast-math mode can break ESPResSo. It is incompatible with the ADDITIONAL_CHECKS feature due to the loss of precision in the LB code on CPU. The Clang 10 compiler breaks field couplings with -ffast-math. The Intel compiler enables the -fp-model fast=1 flag by default; it can be disabled by adding the -fp-model=strict flag.

ESPResSo currently doesn’t fully support link-time optimization (LTO).

2.4.5. Configuring without a network connection

Several external features in ESPResSo rely on external libraries that are downloaded automatically by CMake. When a network connection cannot be established due to firewall restrictions, the CMake logic needs editing:

  • WITH_HDF5: when cloning ESPResSo, the libs/h5xx folder will be a git submodule containing a .git subfolder. To prevent CMake from updating this submodule with git, delete the corresponding command with:

    sed -i '/execute_process(COMMAND ${GIT_EXECUTABLE} submodule update -- libs\/h5xx/,+1 d' CMakeLists.txt

    When installing a release version of ESPResSo, no network communication is needed for HDF5.

  • WITH_STOKESIAN_DYNAMICS: this library is installed using FetchContent. The repository URL can be found in the GIT_REPOSITORY field of the corresponding FetchContent_Declare() command. The GIT_TAG field provides the commit. Clone this repository locally next to the ESPResSo folder and edit the ESPResSo build system such that GIT_REPOSITORY points to the absolute path of the Stokesian Dynamics clone, for example with:

    sed -ri 's|GIT_REPOSITORY +.+stokesian-dynamics.git|GIT_REPOSITORY /work/username/stokesian_dynamics|' CMakeLists.txt

2.5. Compiling, testing and installing

The command make is mainly used to compile the source code, but it can do a number of other things. The generic syntax of the make command is:

make [options] [target] [variable=value]

When no target is given, the target all is used. The following targets are available:

all

Compiles the complete source code. The variable can be used to specify the name of the configuration header to be used.

check

Runs the testsuite. By default, all available tests will be run on 1, 2, 3, 4, 6, or 8 processors.

test

Do not use this target, it is a broken feature (see issue #4370). Use make check instead.

clean

Deletes all files that were created during the compilation.

install

Install ESPResSo in the path specified by the CMake variable CMAKE_INSTALL_PREFIX. The path can be changed by calling CMake with cmake .. -DCMAKE_INSTALL_PREFIX=/path/to/espresso. Do not use make DESTDIR=/path/to/espresso install to install to a specific path, this will cause issues with the runtime path (RPATH) and will conflict with the CMake variable CMAKE_INSTALL_PREFIX if it has been set.

doxygen

Creates the Doxygen code documentation in the doc/doxygen subdirectory.

sphinx

Creates the sphinx code documentation in the doc/sphinx subdirectory.

tutorials

Creates the tutorials in the doc/tutorials subdirectory.

doc

Creates all documentation in the doc subdirectory (only when using the development sources).

A number of options are available when calling make. The most interesting option is probably -j num_jobs, which can be used for parallel compilation. num_jobs specifies the maximal number of concurrent jobs that will be run. Setting num_jobs to the number of available processors speeds up the compilation process significantly.

2.6. Troubleshooting

If you encounter issues when building ESPResSo or running it for the first time, please have a look at the Installation FAQ on the wiki. If you still didn’t find an answer, see Community support.

Many algorithms require parameters that must be provided within valid ranges. Range checks are implemented to catch invalid input values and generate meaningful error messages, however these checks cannot always catch errors arising from an invalid combination of two or more features. If you encounter issues with a script, you can activate extra runtime checks by enabling C++ assertions. This is achieved by updating the CMake project and rebuilding ESPResSo with:

cmake . -DCMAKE_BUILD_TYPE=RelWithAssert
make -j

The resulting build will run slightly slower, but will produce an error message for common issues, such as divisions by zero, array access out of bounds, or square roots of negative numbers.

If this still doesn’t help, you can activate debug symbols to help with instrumentation:

cmake . -DCMAKE_BUILD_TYPE=Debug
make -j

The resulting build will be quite slow but will allow many debugging tools to be used. For details, please refer to chapter Debugging ESPResSo.

If you are dealing with a segmentation fault or undefined behavior, and GDB doesn’t help or is too cumbersome to use (e.g. in MPI-parallel simulations), you can as a last resort activate sanitizers:

cmake . -DWITH_ASAN=ON -DWITH_UBSAN=ON -DCMAKE_BUILD_TYPE=Release
make -j

The resulting build will be around 5 times slower that a debug build, but it will generate valuable reports when detecting fatal exceptions. For more details, please consult the online documentation of UBSAN and ASAN.

1

https://espressomd.org

2

https://git-scm.com/

3

https://github.com/espressomd/espresso

4

https://cmake.org/

5

https://www.fftw.org/