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: https://www5.in.tum.de/mardyn/doxygen_doc/html/

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:

• FFTW3: http://www.fftw.org
• VTK: http://www.vtk.org
• QuickSched: https://arxiv.org/abs/1601.05384

Installation (make)

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

Installing ls1-MarDyn using cmake

Configuration

Initial support to build ls1-mardyn using cmake has been recently added. To build mardyn using cmake first create an additional directory on the root 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 mardyn should be built:

CC=clang CXX=clang++ cmake ..
# or using mpi:
CC=`which mpicc` CXX=`which mpicxx` cmake ..

Specifying the compiler 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.

Finally, build ls1-mardyn using:

make

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

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.

Detailed help can be obtained by running

MarDyn --help

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 (https://github.com/AutoPas/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 at: https://www5.in.tum.de/AutoPas/doxygen_doc/master/namespaceautopas_1_1options.html and within the readXML method of https://www5.in.tum.de/mardyn/doxygen_doc/html/classAutoPasContainer.html

Limitations

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

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

• http://www.ls1-mardyn.de : the official ls1-MarDyn web page.
• mailto:[email protected] : can be used for general questions around ls1-MarDyn.
• mailto:[email protected] : can be used to reach the developers of ls1-MarDyn.