背景信息

LAMMPS全稱Large-scale Atomic Molecular Massively Parallel Simulator，是一款經典分子動力學軟件，用于模擬液態、固態或氣態的粒子集合，廣泛應用于材料、物理、化學等模擬場景。

準備工作

● 已創建彈性高性能計算E-HPC集群。

● 已創建集群用戶。

● 需要安裝的軟件：安裝Intel OneAPI、準備LAMMPS安裝包。

操作步驟

1.編譯。

# 加載Intel工具包中的環境變量
module?load?libpmi/4.1.2/gcc-4.8.5?compiler-rt/2022.1.0?mpi/2021.6.0?mkl/2022.1.0?icc/2022.1.0?gcc/11.4.0

#?下載LAMMPS源代碼壓縮包
wget?-P?/share?//lammps.sandia.gov/tars/lammps-2Aug2023.tar.gz

#?解壓LAMMPS源代碼
tar?xf?lammps.tar.gz?-C?/share

cd?/share/lammps-2Aug2023/src

#?進入/mnt/lammps-2Aug2023/src/MAKE/OPTIONS目錄，修改Makefile.intel_cpu_intelmpi
vi?MAKE/OPTIONS/Makefile.intel_cpu_intelmpi
#?在OPTFLAGS?中增加以下內容
-O3?-g?-DLAMMPS_BIGBIG?-DLAMMPS_MEMALIGN=64

#?編譯
make?-j?$(nproc)?yes-most
make?-j?$(nproc)?yes-intel
make?-j?$(nproc)?intel_cpu_intelmpi

#?運行測試
mpirun?-np?2?lmp_intel_cpu_intelmpi?-sf?intel?-in?-pk?intel?/share/lammps-28Mar2023/examples/melt/in.melt

2.運行測試文件。

編輯 in.lj.billion文件如下所示：

#?3d?Lennard-Jones?melt

variable????????x?index?20
variable????????y?index?20
variable????????z?index?20

variable????????xx?equal?20*$x
variable????????yy?equal?20*$y
variable????????zz?equal?20*$z

units???????????lj
atom_style??????atomic

lattice?????????fcc?0.8442
region??????????box?block?0${xx}0${yy}0${zz}
create_box??????1?box
create_atoms????1?box
mass????????????11.0

velocity????????all?create?1.4487287?loop?geom

pair_style??????lj/cut?2.5
pair_coeff??????111.01.02.5

neighbor????????0.3?bin
neigh_modify????delay?0?every?20?check?no

fix?????????????1?all?nve

run?????????????100

撰寫slurm腳本：

#!/bin/bash
#SBATCH?-N?2
#SBATCH?--partition=debug
#SBATCH?--exclusive
#SBATCH?-J?lammps_bench
#SBATCH?-o?test_lammps.%J.out
#SBATCH?-e?test_lammps.%J.err
#SBATCH?--time=00:5:00

#module
module?load?gcc?compiler-rt/2022.1.0?icc/2022.1.0?mpi/2021.6.0?mkl

#config?openmp
exportOMP_NUM_THREADS=1
exportOMP_PROC_BIND=true
exportOMP_PLACES=cores

#config?mpi
exportI_MPI_PMI_LIBRARY=libpmi2.so
exportUCX_NET_DEVICES=mlx5_0:1,mlx5_3:1
exportSLURM_MPI_TYPE=pmi2

#run?application
srun??--ntasks-per-node=56?--cpus-per-task=2?--cpu-bind=cores?-m?plane=56?/share/user01/lammps-28Mar2023/build/lmp?-sf?intel?-in?in.lj.billion

3.查看最終結果。

LAMMPS?(28?Mar?2023)
??using?1?OpenMP?thread(s)?per?MPI?task
Lattice?spacing?in?x,y,z?=1.67959621.67959621.6795962
Created?orthogonal?box?=(000)?to?(671.83848671.83848671.83848)
4?by?4?by?7?MPI?processor?grid
Created?256000000?atoms
??using?lattice?unitsin?orthogonal?box?=(000)?to?(671.83848671.83848671.83848)
??create_atoms?CPU?=0.230?seconds
----------------------------------------------------------
Using?INTEL?Package?without?Coprocessor.
Compiler:?Intel?Classic?C++?20.21.6?/?Intel(R)?C++?g++?11.4?mode
SIMD?compiler?directives:?Enabled
Precision:?mixed
----------------------------------------------------------
Generated?0?of?0?mixed?pair_coeff?terms?from?geometric?mixing?rule
Neighbor?list?info?...
??update:?every?=20?steps,?delay?=0?steps,?check?=?no
??max?neighbors/atom:?2000,?page?size:?100000
??master?list?distance?cutoff?=2.8
??ghost?atom?cutoff?=2.8
??binsize?=1.4,?bins?=480480480
1?neighbor?lists,?perpetual/occasional/extra?=100
(1)?pair?lj/cut/intel,?perpetual
??????attributes:?half,?newton?on,?intel
??????pair?build:?half/bin/newton/intel
??????stencil:?half/bin/3d
??????bin:?intel
Setting?up?Verlet?run?...
??Unit?style????:?lj
??Current?step??:0
??Time?step?????:0.005
Per?MPI?rank?memory?allocation?(min/avg/max)=3295|3343|3463?Mbytes
???Step??????????Temp??????????E_pair?????????E_mol??????????TotEng?????????Press
01.44??????????-6.7733673??????0?????????????-4.6133673?????-5.0196698
1000.7594409?????-5.7614765??????0?????????????-4.6223152??????0.18996685
Loop?time?of?67.0307?on?112?procs?for100?steps?with?256000000?atoms

Performance:?644.481?tau/day,?1.492?timesteps/s,?381.915?Matom-step/s
99.6%?CPU?use?with?112?MPI?tasks?x?1?OpenMP?threads
...