MD-Bench/README.md

MD-Bench

A generic proxy-app toolbox for state-of-the-art molecular dynamics algorithms

Build instructions for the lammps variant

Properly configure your building by changing config.mk file. The following options are available:

• TAG: Compiler tag (available options: GCC, CLANG, ICC, ONEAPI, NVCC).
• ISA: Instruction set (available options: SSE, AVX, AVX2, AVX512).
• MASK_REGISTERS: Use AVX512 mask registers (always true when ISA is set to AVX512).
• OPT_SCHEME: Optimization algorithm (available options: lammps, gromacs).
• ENABLE_LIKWID: Enable likwid to make use of HPM counters.
• DATA_TYPE: Floating-point precision (available options: SP, DP).
• DATA_LAYOUT: Data layout for atom vector properties (available options: AOS, SOA).
• ASM_SYNTAX: Assembly syntax to use when generating assembly files (available options: ATT, INTEL).
• DEBUG: Toggle debug mode.
• EXPLICIT_TYPES: Explicitly store and load atom types.
• MEM_TRACER: Trace memory addresses for cache simulator.
• INDEX_TRACER: Trace indexes and distances for gather-md.
• COMPUTE_STATS: Compute statistics.

Configurations for LAMMPS Verlet Lists optimization scheme:

• ENABLE_OMP_SIMD: Use omp simd pragma on half neighbor-lists kernels.
• USE_SIMD_KERNEL: Compile kernel with explicit SIMD intrinsics.

Configurations for GROMACS MxN optimization scheme:

• USE_REFERENCE_VERSION: Use reference version (only for correction purposes).
• XTC_OUTPUT: Enable XTC output.
• HALF_NEIGHBOR_LISTS_CHECK_CJ: Check if j-clusters are local when decreasing the reaction force.

Configurations for CUDA:

• USE_CUDA_HOST_MEMORY: Use CUDA host memory to optimize host-device transfers.

You can clean intermediate build results with make clean, and all build results with make distclean. You have to call make clean before make if you changed the build settings.

Configuration

Currently all settings apart from the options described below are hard-coded in main.c.

Run the benchmark

Without any options 200 steps with system size 32x32x32 is used.

The default can be changed using the following options:

-n / --nsteps <int>:  set number of timesteps for simulation
-nx/-ny/-nz <int>:    set linear dimension of systembox in x/y/z direction