Faq
在曙光超算中使用
基本使用方法
- 在曙光超算中，已发布版本位于/work/share/ac21ujhbvo/local/mesospire/，用户可查看目录获取最新版本。
- 激活方式为
source /work/share/ac21ujhbvo/local/mesospire/20xxxxxx/env.sh - 运行
mesospire_info可以确认程序中包含最新版本更新信息。
1. 参数输入及输入文件创建
mesospire_shell 提供两种不同输入格式，一种是yaml格式，一种是json格式，用户可以根据自己的喜好选择其中一种格式。下面的例子中，我们将展示两种格式的输入文件。
config.yaml
omp_threads: 64
# 指定采用zjdev中的合金凝固模块
type: AlloySolidification
# 输出结果路径
path: results/NiAlTa-solidification-varD-1
# 是否覆盖已有输出结果
clear: true
# 定义所含元素，最后一个为溶剂
elements: [AL, TA, NI]
mesh:
nx: 150
ny: 150
nz: 1
dx: 5.0e-07
dt: 1.0e-06
current_time: 0
simulation_time: 100
parameter:
T: 1649.85
P: [1.64e-07, 6.69e-08]
Vm: 1.0e-05
mu: 6.02e-10
sigma: 0.3
eta: 2.5e-06
phase:
# 液相的能量及扩散系数输入
liquid:
type: MultiComponentCustomPhase
name: liquid
element: [AL, TA]
gibbs_energy:
type: NiAlTaLIQUIDGibbsEnergy
diffusion_potential:
type: NiAlTaLIQUIDDiffusionPotential
diffusivity:
type: NiAlTaLIQUIDDiffusivity
# 固相的能量及扩散系数输入
solid:
type: MultiComponentCustomPhase
name: solid
element: [AL, TA]
gibbs_energy:
type: NiAlTaFCCGibbsEnergy
diffusion_potential:
type: NiAlTaFCCDiffusionPotential
diffusivity:
type: NiAlTaFCCDiffusivity
boundary_condition:
BC0X:
type: PERIODIC
BCNX:
type: PERIODIC
BC0Y:
type: PERIODIC
BCNY:
type: PERIODIC
nucleation:
- type: SetWhole
variable:
- varname: phi
value: [1, 0]
- varname: c_liquid
value: [0.131, 0.051]
- varname: c_solid
value: [0.131, 0.051]
- type: SetSphere
point: [75, 75, 0]
radius: 1
smooth: true
smooth_variable: phi
width: 6
variable:
- varname: phi
value: [0, 1]
- varname: c_liquid
value: [0.131, 0.051]
- varname: c_solid
value: [0.131, 0.051]
# 各向异性参数
anisotropy:
type: CubicAnisotropyYang
parameters: [0.3]
mobility: [0.3]
output:
initial_time: 0
final_time: 10
# 输出模拟结果的初始时间
initial_interval: 0.001
every_number: 10
factor: 2
variable: []
information:
- 1.0e-10
- 30000
- 0.02
config.json
{
"omp_threads": 64,
"type": "AlloySolidification",
"path": "results/NiAlTa-solidification-varD-1",
"clear": true,
"mesh": {
"nx": 150,
"ny": 150,
"nz": 1,
"dx": 5e-07,
"dt": 1e-06,
"current_time": 0,
"simulation_time": 100.0
},
"parameter": {
"T": 1649.85,
"P": [1.64e-7, 6.69e-8],
"Vm": 1e-05,
"mu": 6.02e-10,
"sigma": 0.3,
"eta": 25.0e-7
},
"phase": {
"liquid": {
"type": "MultiComponentCustomPhase",
"name": "liquid",
"element": ["AL", "TA"],
"gibbs_energy": {"type": "NiAlTaLIQUIDGibbsEnergy"},
"diffusion_potential": {"type": "NiAlTaLIQUIDDiffusionPotential"},
"diffusivity": {"type": "NiAlTaLIQUIDDiffusivity"}
},
"solid": {
"type": "MultiComponentCustomPhase",
"name": "solid",
"element": ["AL", "TA"],
"gibbs_energy": {"type": "NiAlTaFCCGibbsEnergy"},
"diffusion_potential": {"type": "NiAlTaFCCDiffusionPotential"},
"diffusivity": {"type": "NiAlTaFCCDiffusivity"}
}
},
"boundary_condition": {
"BC0X": {"type": "PERIODIC"},
"BCNX": {"type": "PERIODIC"},
"BC0Y": {"type": "PERIODIC"},
"BCNY": {"type": "PERIODIC"}
},
"nucleation": [
{
"type": "SetWhole",
"variable": [
{
"varname": "phi",
"value": [1.0, 0.0]
},
{
"varname": "c_liquid",
"value": [0.131, 0.051]
},
{
"varname": "c_solid",
"value": [0.131, 0.051]
}
]
},
{
"type": "SetSphere",
"point": [75, 75, 0],
"radius": 1,
"smooth": true,
"smooth_variable": "phi",
"width": 6,
"variable": [
{
"varname": "phi",
"value": [0.0, 1.0]
},
{
"varname": "c_liquid",
"value": [0.131, 0.051]
},
{
"varname": "c_solid",
"value": [0.131, 0.051]
}
]
}
],
"anisotropy": {
"type": "CubicAnisotropyYang",
"parameters": [0.3],
"mobility": [0.3]
},
"output": {
"initial_time": 0,
"final_time": 10.0,
"initial_interval": 1e-03,
"every_number": 10,
"factor": 2,
"variable": []
},
"elements": [
"AL",
"TA",
"NI"
],
"information": [
1.0e-10,
3.0e4,
0.02
]
}
2. 运行脚本及命令
2.1 直接提交
任务提交命令为：
sbatch sumbit_sugon.sh
submit_sugon_direct.sh
#!/bin/sh
#SBATCH --job-name=phasefield
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=64
#SBATCH --partition=wzhcnormal
#SBATCH --time=6:00:00
#SBATCH --output=phasefield.out
source /work/share/ac21ujhbvo/local/mesospire/20230804/env.sh
mesospire_shell -i config.yaml
2.2 便捷提交
任务提交命令为：
bash sumbit_sugon.sh config
submit_sugon.sh
#!/bin/bash
# if not argument, print usage
if [ $# -eq 0 ]; then
# echo "Usage: ./submit_sugon.sh [input_file_name]"
echo -e "\033[34mUsage: ./submit_sugon.sh [input_file_name]\033[0m"
exit 1
fi
# if input file not exist, print error
if [ ! -f "$1.yaml" ]; then
echo -e "\033[31mError: $1.yaml not exist\033[0m"
exit 1
fi
# thread_num variable, default 64. if the second argument is not empty, use it as thread_num
thread_num=64
if [ ! -z "$2" ]; then
thread_num=$2
fi
echo -e "\033[32mCurrent thread number: $thread_num\033[0m"
echo -e "\033[32mCurrent task name: $1, it will be submitted to sugon.\033[0m"
sbatch <<EOT
#!/bin/sh
#SBATCH --job-name=$1
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=$thread_num
#SBATCH --partition=wzhcnormal
#SBATCH --time=6:00:00
#SBATCH --output=$1.out
module load compiler/intel/2021.3.0
module load compiler/gcc/9.3.0
export CXX=/public/software/compiler/intel-compiler/2021.3.0/bin/intel64/icpc
export CC=/public/software/compiler/intel-compiler/2021.3.0/bin/intel64/icc
app_path=../../build/bin/mesospire_shell
\${app_path} -i $1.yaml
EOT
squeue -i 5