MiniMD Save

MiniMD Molecular Dynamics Mini-App

Project README

miniMD is a simple, parallel molecular dynamics (MD) code. miniMD is an MD microapplication in the Mantevo project at Sandia National Laboratories ( ). The primary authors of miniMD are Steve Plimpton, Paul Crozier ([email protected]) and Christian Trott ([email protected]).

Copyright (2008) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains certain rights in this software. This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.

This library 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 Lesser General Public License for more details.

You should have received a copy of the GNU Lesser General Public License along with this software; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA. See also: .

For questions, contact Christian Trott ([email protected]).

Please read the accompanying README and LICENSE files.


miniMD is a parallel molecular dynamics (MD) simulation package written in C++ and intended for use on parallel supercomputers and new architechtures for testing purposes. The software package is meant to
be simple, lightweight, and easily adapted to new hardware. It is designed following many of the same algorithm concepts as our LAMMPS ( parallel MD code, but is much simpler.

Authors: Steve Plimpton, Paul Crozier ([email protected]) and Christian Trott ([email protected])

This simple code is a self-contained piece of C++ software that performs parallel molecular dynamics simulation of a Lennard-Jones or a EAM system and gives timing information.

It is implemented to be very scalable (in a weak sense). Any reasonable parallel computer should be able to achieve excellent scaled speedup (weak scaling). miniMD uses a spatial decomposition parallelism and has many other similarities to the much more complicated LAMMPS MD code:

The sub-directories contain different variants of miniMD:

miniMD_ref: supports MPI+OpenMP hybrid mode. miniMD_OpenCL: an OpenCL version of miniMD, uses MPI to parallelize over multiple devices. Limited Features. There is an issue with running larger system then -s 39. Other problems exist with double precision support. miniMD_Kokkos: supports MPI and uses Kokkos on top of it, compiles with pThreads, OpenMP or CUDA backend miniMD_KokkosLambda: another Kokkos variant making extensive use of C++11 miniMD_Intel: supports MPI+OpenMP hybrid mode. Optimized by Intel. Comes with an intrinsic version of the LJ-force kernel and the neighborlist construction for Xeon Phi. miniMD_OpenACC: supports MPI+OpenACC hybrid mode.

Each variant is self contained and does not reference any source files of the other variants.

Strengths and Weaknesses:

miniMD consists of less than 5,000 lines of C++ code. Like LAMMPS, miniMD uses spatial decomposition MD, where individual processors in a cluster own subsets of the simulation box. And like LAMMPS, miniMD enables users to specify a problem size, atom density, temperature, timestep size, number of timesteps to perform, and particle interaction cutoff distance. But compared to LAMMPS, MiniMD's feature set is extremely limited, and only two types interactions (Lennard-Jones/ EAM) are available. No long-range electrostatics or molecular force field features are available. Inclusion of such features is unnecessary for testing basic MD and would have made miniMD much bigger, more complicated, and harder to port to novel hardware. The current version of LAMMPS includes over 200,000 lines of code in hundreds of files, nineteen optional packages, over one hundred different commands, and over five hundred pages of documentation. Such a large and complicated code is not ideally suited for answering certain performance questions or for tinkering by non-MD-experts. The biggest difference to LAMMPS in terms of performance is caused by using only a single atom-type. Thus all force parameter lookups are simple variable references, while in LAMMPS they are gather operations. On architectures with slow vector-gather operations, this can cause signifcant performance differences between miniMD and LAMMPS.

MiniMD uses neighborlists for the force calculation, as opposed to cell lists which are employed by for example COMD. The neighborlist approach (or variants of it) are used by most commonly used MD applications, such as LAMMPS, Amber and NAMD. Cell lists are employed by some specialised codes, in particular for very large scale simulations which might be memory capacity limited. With neighborlists the memory footprint of a simulation is significantly larger, though with about 500,000 atoms per GB it is still small compared to many other applications. On the other hand the number of distance checks in the neighborlist approach is much smaller than with cell lists. For neighborlists the distances to all atoms in a volume of 4/3PIr_cut^3, r_cut being the neighbor cutoff distance, have to be checked. With celllists that volume is 27*r_cut^3. While the latter approach makes the data access for positions coalesced reads, as opposed to random reads with neighborlists, on most architectures this is not enough of an advantage to compensate for the ~6x difference in distance checks.

In versions >=2.x miniMD now simulates the behaviour of having multiple atom types. Mostly this means that certain variable accesses such as force parameters and cutoffs are now replaced by table lookups. This will reduce performance compared to 1.x variants of miniMD. It will also hinder vectorization more. On the upside this change closes the biggest gap between the miniApp and what happens in real apps. In fact the performance differenc with LAMMPS was significantly reduced.

Compiling the code:

There is a simple Makefile that should be easily modified for most Unix-like environments. There are also one or more Makefiles with extensions that indicate the target machine and compilers. Read the Makefile for further instructions. If you generate a Makefile for your platform and care to share it, please send it to Paul Crozier: [email protected] . By default the code compiles with MPI support and can be run on one or more processors. There is also a Makefile.default which should NOT require a GNU Make compatible make.



Get info on all options, and targets

make -f Makefile.default

Build with simplified Makefile, using defaults for a CPU system


Note, when building the KokkosArray variant directly out of the svn repository you need to do

make SVN=yes

for building miniMD_KokkosArray.

Furthermore miniMD_ref and miniMD_KokkosArray support both single and double precision builds. Single precision can be triggered by using SP=yes/no in the make command-line (e.g. make openmpi SP=yes).

Other options are: DEBUG=yes -- enable debugmode AVX=yes -- enable compilation for avx [DEFAULT] KNC=yes -- enable compilation for Xeon Phi SIMD=yes -- use #pragma simd for some kernels [DEFAULT] PAD=[3/4] -- pad arrays to 3 or 4 elements RED_PREC=yes -- enable fast_math and similar (reduced precision divide) GSUNROLL=yes -- unroll gather and scatter (for Xeon Phi only) [DEFAULT] SP=yes -- use single precision
LIBRT=yes -- use librt timers (more precise)

For KokkosArray Variant only: KOKKOSPATH=path -- path to the Kokkos core source directory (kokkos/core/src) OMP=yes -- use OpenMP (if not use PThread) [DEFAULT] HWLOC=yes -- use HWLOC for thread pinning HWLOCPATH=path -- path to HWLOC library when building with HWLOC support
CUDA=yes -- build with cuda support (works only with the cuda target) CUDAARCH=sm_xx -- set GPU architecture target (default sm_35)

Typical choices:

CPUS: make openmpi -j 16

Xeon Phi make intel KNC=yes -j 16

Build with pthreads [KokkosArray Variant only: make openmpi OMP=no HWLOC=yes KOKKOSPATH=/usr/local/kokkos/core/src -j 16

==To remove all output files, type:

make clean_


make clean


make test

The test will run a simulation and compare it against reference output. Where are different test modes, which change the amount of tests run. Running 'make test' will give instructions how to run more complex tests. Note the test does not currently run with multiple GPUs since it does not provide the necessary environment variables.

Running the code and sample I/O:


miniMD (serial mode)

mpirun -np numproc miniMD (MPI mode)


mpirun -np 16 ./miniMD

MiniMD understands a number of command-line options. To get the options for each particular variant of miniMD please use "-h" as an argument.

You will also need to provide a simple input script, which you can model after the ones included in this directory (e.g. in.lj.miniMD). The format and parameter description is as follows:

Sample input file contents found in "":

Lennard-Jones input file for MD benchmark

lj units (lj or metal) none data file (none or filename)
lj force style (lj or eam) 1.0 1.0 force parameters for LJ (epsilon, sigma) 32 32 32 size of problem 100 timesteps 0.005 timestep size 1.44 initial temperature 0.8442 density 20 reneighboring every this many steps 2.5 0.30 force cutoff and neighbor skin 100 thermo calculation every this many steps (0 = start,end)

Sample output file contents found in "out.lj.miniMD":

Create System:

Done ....

miniMD-Reference 1.2 (MPI+OpenMP) output ...

Run Settings:

# MPI processes: 2
# OpenMP threads: 16
# Inputfile: in.lj.miniMD
# Datafile: None

Physics Settings:

# ForceStyle: LJ
# Force Parameters: 1.00 1.00
# Units: LJ
# Atoms: 864000
# System size: 100.78 100.78 100.78 (unit cells: 60 60 60)
# Density: 0.844200
# Force cutoff: 2.500000
# Timestep size: 0.005000

Technical Settings:

# Neigh cutoff: 2.800000
# Half neighborlists: 0
# Neighbor bins: 50 50 50
# Neighbor frequency: 20
# Sorting frequency: 20
# Thermo frequency: 100
# Ghost Newton: 1
# Use intrinsics: 0
# Do safe exchange: 0
# Size of float: 8

Starting dynamics ...

Timestep T U P Time

0 1.440000e+00 -6.773368e+00 -5.019671e+00 0.000 100 7.310629e-01 -5.712170e+00 1.204577e+00 3.650

Performance Summary:

MPI_proc OMP_threads nsteps natoms t_total t_force t_neigh t_comm t_other performance perf/thread grep_string t_extra

2 16 100 864000 3.649762 2.584821 0.735003 0.145945 0.183993 23672777.021430 739774.281920 PERF_SUMMARY 0.035863

Running on GPUs with Kokkos

The Kokkos variant needs a CUDA aware MPI for running on GPUs (though it might work on a single GPU with any MPI). Currently known MPI implementations with CUDA support are: mvapich2 1.8 or higher openmpi 1.7 or higher cray mpi on XK7 and higher

Note those typically require some environment variables to be set. For example mvapich2 1.9 can be used like this: mpiexec -np 2 -env MV2_USE_CUDA=1 ./miniMD_mvapichcuda --half_neigh 0 -s 60

When compiling for GPU Architectures prior to Kepler (sm_21 or lower) you need to put -DUSE_TEXTURE_REFERENCES in the compiler flags to use Texture Memory during the force calculations. If not you loose about 70% of your performance.

Known Issues:

The OpenCL variant does not currently support all features of the Reference and Kokkos variant. In particular it does not support EAM simulations. Also due to limitations in OpenCL (and the author not having the time to work around them) the simulations are limited to about 240k atoms in the standard LJ settings. This corresponds to -s 39.

Running the in.*-data.miniMD inputs on the GPU with the Kokkos variant defaults to too many neighbor bins. This causes significantly increased memory consumption and longer runtimes. Use -b 30 as a command line option, to override the default neighbor bin size.

The option --safe_exchange is currently not active in publicly available builds.

Open Source Agenda is not affiliated with "MiniMD" Project. README Source: Mantevo/miniMD
Open Issues
Last Commit
1 year ago

Open Source Agenda Badge

Open Source Agenda Rating