51 lines
2.3 KiB
Markdown
51 lines
2.3 KiB
Markdown
# MD-Bench
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A generic proxy-app toolbox for state-of-the-art molecular dynamics algorithms
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## Build instructions for the lammps variant
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Properly configure your building by changing `config.mk` file. The following options are available:
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- **TAG:** Compiler tag (available options: GCC, CLANG, ICC, ONEAPI, NVCC).
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- **ISA:** Instruction set (available options: SSE, AVX, AVX2, AVX512).
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- **MASK\_REGISTERS:** Use AVX512 mask registers (always true when ISA is set to AVX512).
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- **OPT\_SCHEME:** Optimization algorithm (available options: lammps, gromacs).
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- **ENABLE\_LIKWID:** Enable likwid to make use of HPM counters.
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- **DATA\_TYPE:** Floating-point precision (available options: SP, DP).
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- **DATA\_LAYOUT:** Data layout for atom vector properties (available options: AOS, SOA).
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- **ASM\_SYNTAX:** Assembly syntax to use when generating assembly files (available options: ATT, INTEL).
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- **DEBUG:** Toggle debug mode.
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- **EXPLICIT\_TYPES:** Explicitly store and load atom types.
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- **MEM\_TRACER:** Trace memory addresses for cache simulator.
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- **INDEX\_TRACER:** Trace indexes and distances for gather-md.
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- **COMPUTE\_STATS:** Compute statistics.
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Configurations for LAMMPS Verlet Lists optimization scheme:
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- **ENABLE\_OMP\_SIMD:** Use omp simd pragma on half neighbor-lists kernels.
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- **USE\_SIMD\_KERNEL:** Compile kernel with explicit SIMD intrinsics.
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Configurations for GROMACS MxN optimization scheme:
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- **USE\_REFERENCE\_VERSION:** Use reference version (only for correction purposes).
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- **XTC\_OUTPUT:** Enable XTC output.
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- **HALF\_NEIGHBOR\_LISTS\_CHECK\_CJ:** Check if j-clusters are local when decreasing the reaction force.
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Configurations for CUDA:
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- **USE\_CUDA\_HOST\_MEMORY:** Use CUDA host memory to optimize host-device transfers.
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You can clean intermediate build results with `make clean`, and all build results with `make distclean`.
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You have to call `make clean` before `make` if you changed the build settings.
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## Configuration
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Currently all settings apart from the options described below are hard-coded in `main.c`.
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## Run the benchmark
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Without any options 200 steps with system size 32x32x32 is used.
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The default can be changed using the following options:
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```
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-n / --nsteps <int>: set number of timesteps for simulation
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-nx/-ny/-nz <int>: set linear dimension of systembox in x/y/z direction
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```
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