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Update README.md with config.mk options

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Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
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Rafael Ravedutti 2022-09-29 12:21:29 +02:00
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# MD-Bench
A simple, sequential C implementation short range MD algorithms.
A generic proxy-app toolbox for state-of-the-art molecular dynamics algorithms
## Build instructions for the lammps variant
1. Open `config.mk` and edit the `TAG` value according to the tool chain used. Currently supported is GCC, CLANG (LLVM), and ICC (Intel).
2. Change `DATA_LAYOUT` and `DATA_TYPE` if desired in config.mk.
3. Open and adapt the compiler flags in `<include_<TOOLCHAIN>.mk`, e.g. in `include_ICC.mk` for the Intel tool chain.
4. Build the binary calling `make`.
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.