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ls1-MarDyn Overview

ls1-MarDyn is a massively parallel Molecular Dynamics (MD) code for large systems. Its main target is the simulation of thermodynamics and nanofluidics. ls1-MarDyn is designed with a focus on performance and easy extensibility.

Getting Started

Documentation

The current doxygen documentation can be found here.

Prerequisites

mandatory requirements

  • a C++17 compiler (GCC, Clang, Intel, PGI, Cray, NEC SX, IBM XL, ...)
  • a working MPI installation compatible with the MPI 3.0 specification or later (Open MPI, MPICH, MVAPICH, Intel MPI, Cray MPI, NEC MPI, IBM Platform MPI, ...)

optional requirements

Installation

Installing ls1-MarDyn using cmake

This is the recommended way of building ls1-MarDyn.

Quick guide

Run the following commands to build ls1-MarDyn with the Clang compiler. Adjust options (e.g. ENABLE_MPI) according to the individual needs.

mkdir build
cd build
CC=clang CXX=clang++ ccmake ..
make -j $(nproc)

Detailed guide

To build ls1-MarDyn using cmake first create an additional directory on the root ls1-MarDyn directory and change into that directory.

mkdir build
cd build

Next, cmake has to be executed. In most cases, you will have to specify the compiler with which ls1-MarDyn should be built:

CC=clang CXX=clang++ cmake ..

Some of the most common compilers are

Compiler CC CXX
GCC gcc g++
Intel oneAPI icx icpx
Clang clang clang++

The Intel Classic Compiler (icc and icpc) is not recommended to use, since it is deprecated and does not work with AutoPas.

Note: The Intel oneAPI compiler may rely on some external C++ libraries shipped with gcc (see this issue for details).

Specifying the compiler this way is only possible at the first execution of cmake. If you want to change the compiler later on, either add another build directory, or first clear the existing build directory.

To configure the options within ls1-MarDyn it is recommended to use ccmake:

ccmake ..

That way you can easily edit the available options.

Alternatively, specify the configuration with use of the cmake command:

CC=clang CXX=clang++ cmake -DENABLE_MPI=ON ..

Finally, build ls1-MarDyn using:

make

For a faster build, you can make use of parallel building:

make -j $(nproc)

The executable is then found at build/src/MarDyn.

Installing ls1-MarDyn using make

ls1-MarDyn is build from source code using GNU make or alternatively using cmake (see below).

A default build using the GNU compiler and a MPI library providing the mpicxx compiler wrapper is done with

  cd src
  make

To get an overview of options to control the build process, e.g. to use another compiler, disable MPI, ... run

  make help

To see a list of all supported target platforms and compilers call

  make cfg_list

and run then make with the desired configuration:

  make CFG=<config name>

To display further information about the available suboptions for a configuration use

  make CFG=<cfg name> cfg_help

ADIOS2 support

If a visualisation with MegaMol and ADIOS2 is desired, an installation of ADIOS2 is needed. By default, ADIOS2 is downloaded and built automatically during the build process of ls1-MarDyn. If connections to external resources, e.g. on HPC systems, are blocked, the following steps (for an MPI build) are required to build ls1-MarDyn with ADIOS2. Download ADIOS2 locally

git clone https://github.com/ornladios/ADIOS2.git ADIOS2

It may be required to checkout the correct version of ADIOS2:

cd ADIOS2
git checkout v2.7.1.436

Upload it together with ls1-MarDyn to the target HPC system. On the HPC system, after loading the proper modules, create a build folder in the ADIOS2 directory and run cmake. Note: The PATH-TO-ADIOS2 string must be adjusted.

cd ADIOS2
mkdir build && cd build
cmake .. -DCMAKE_INSTALL_PREFIX=PATH-TO-ADIOS2/ADIOS2/build/install -DADIOS2_BUILD_EXAMPLES=OFF -DADIOS2_BUILD_TESTING=OFF -DADIOS2_USE_Profiling=OFF -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx

Build now using:

make -j install

The -j parameter can be adjusting to the present system.

After successfully building ADIOS2, ls1-MarDyn can be build. In accordance to the above installation steps (section "Configuration"), an additional build directory in the root directory of ls1-MarDyn must be created. In this directory run cmake. Note: The PATH-TO-ADIOS2 string must be adjusted as it was done before.

mkdir build
cd build
cmake .. -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx -DADIOS2_DIR=PATH-TO-ADIOS2/ADIOS2/build/install/lib64/cmake/adios2 -DENABLE_MPI=ON -DFIND_PACKAGE_ADIOS2=ON

Finally, build ls1-MarDyn using:

make

For a parallel and faster build please use make's -j parameter with an appropriate number of tasks.

Note: For both, ADIOS2 and ls1-MarDyn, ccmake can be used to configure options.

Running ls1-MarDyn

The basic command to run ls1-MarDyn is as follows:

MarDyn [options] <inputfile>

where MarDyn is the executable build in the INSTALLATION section, [options] are any "--"-prefixed options as listed by MarDyn --help and <inputfile> is a input file.

To get an overview of further command line options run

MarDyn --help

To understand how to write an input file check out examples/all-options.xml, the various examples in the examples folder and the documentation of the various readXML() methods, e.g. via our doxygen documentation.

running examples

ls1-MarDyn comes with a set of examples, which can be found in the examples folder.

cd examples/EOX/305K_liq
mpirun -np 2 ../../../src/MarDyn config.xml  --steps 10

optional: to make the simulation aware of time limits like on a compute node, which should stop the simulation even if the desired amount of steps is not reached use loop-abort-time in (s) in XML or CLI:

mpirun -np 2 ../../../src/MarDyn config.xml  --steps 10 --loop-abort-time 3600

AutoPas Support

ls1-MarDyn supports AutoPas as a replacement for the used linked cells container and the built-in force calculation.

Building for AutoPas

To enable support for AutoPas, you will have to enable the option ENABLE_AUTOPAS.

Running using AutoPas

To use AutoPas a few modifications to the normal xml config files have to be performed:

  • The datastructure section has to be changed to type AutoPas.
  • If inside of the datastructure section no additional information is given AutoPas will run without auto-tuning and a linked cells container (rebuild frequency = 1, skin = 0).
  • Multiple further options can be specified for AutoPas. For a quick overview check config_autopas_allOptions.xml in the Argon example directory. Additional information for the options can be found in the official documentation and within the responsible readXML method.

Limitations

  • Using AutoPas, currently, only single-centered Lennard-Jones interactions are possible.

Visualisation

The simulations can be visualised by two external programs which requires the inclusion of the corresponding plugin.

MegaMol

The MegaMol software is developed by VISUS of the University of Stuttgart. Detailed information on how to install it can be found in its GitHub repo. It supports the import of the following two file formats. See doc/visualisation_MegaMol.dox for detailed information.

mmpld

This is the old file format for visualisation. Use the MmpldWriter plugin to write the visualisation files during simulation.

ADIOS2

This kind of visualisation files is recommended. Use the Adios2Writer plugin to write the visualisation files during simulation. The produced files can also be used for a restart (see Adios2Reader).

Paraview

Read the documentation in doc/visualisation_paraview.dox for detailed information.

Additional resources

ls1-MarDyn is documented using doxygen. To build the documentation run

doxygen Doxyfile

It includes information about the following topics

  • \ref ls1MarDynInputFiles Mardyn Input Files
  • \ref unitTests Unit tests
  • \ref visualisation Graphical Simulation Output

as well as the documentation of the source code.

Contact