1 Star 0 Fork 75

shaoyuteng / hpcrunner

forked from openEuler / hpcrunner 
加入 Gitee
与超过 1200万 开发者一起发现、参与优秀开源项目,私有仓库也完全免费 :)
免费加入
克隆/下载
贡献代码
同步代码
取消
提示: 由于 Git 不支持空文件夾,创建文件夹后会生成空的 .keep 文件
Loading...
README
MulanPSL-2.0

HPCRunner : 贾维斯智能助手

愿景:自动容器化助力极简部署,一站式调优HPC应用

项目背景

​ HPC被喻为是IT行业“金字塔上的明珠”,其部署、编译、运行、性能采集分析的门槛非常高,不同的机器上部署HPC应用耗费大量精力,而且很多情况下需要同时部署ARM/X86两套环境进行验证,增加了很多的重复性工作,无法聚焦核心算法优化。

贾维斯

项目特色

  • 支持ARM/X86,一键部署,采用业界权威依赖目录结构管理海量依赖,自动生成module file
  • 根据HPC配置实现一键编译运行、一键CPU/GPU性能采集、一键Benchmark.
  • 所有配置仅用一个文件记录,HPC应用部署到不同的机器仅需修改配置文件.
  • 日志管理系统自动记录HPC应用部署过程中的所有信息.
  • 软件本身无需编译开箱即用,仅依赖Python环境.
  • HPC应用容器化-目前QE已经实现,参考container目录.
  • (未来) 集成HPC领域常用性能调优手段、核心算法.
  • (未来) 集群性能分析工具.
  • (未来) 智能调优.

目录结构

目录/文件 说明 备注
benchmark 矩阵运算、OpenMP、MPI、P2P性能测试
doc 文档
downloads 存放依赖库源码包/压缩包
examples 性能小实验
package 存放安装脚本和FAQ
software 依赖库二进制仓库(内置精度分析工具) 自动生成
src 贾维斯源码
templates 常用HPC应用的配置模板
test 贾维斯测试用例
workloads 常用HPC应用的算例合集
init.sh 贾维斯初始化文件
jarvis 贾维斯启动入口

已验证HPC应用

气象海洋领域:

  • WRF

  • CMAQ

  • fvcom

  • SPECFEM3D_GLOBE

  • udunits

流体力学领域:

  • OpenFOAM

  • SU2

  • miniFE

计算化学领域:

  • CP2K

  • nwchem

  • Amber

  • QE

  • VASP

  • ABINIT

  • SIESTA

量子力学领域:

  • octopus

生命科学领域:

  • bedtools

  • blast

  • bwa

  • gatk

  • octave

  • picard

  • relion

使用说明

1.下载包解压之后初始化

source ./init.sh

2.修改data.config或者套用现有模板,各配置项说明如下所示:

配置项 说明 示例
[SERVER] 服务器节点列表,多节点时用于自动生成hostfile,每行一个节点 11.11.11.11
[DOWNLOAD] 每行一个软件的版本和下载链接,默认下载到downloads目录(可设置别名) cp2k/8.2 https://xxx cp2k.8.2.tar.gz
[DEPENDENCY] HPC应用依赖安装脚本 ./jarvis -install gcc/9.3.1 com
module use ./software/modulefiles
module load gcc9
[ENV] HPC应用编译运行环境配置 source env.sh
[APP] HPC应用信息,包括应用名、构建路径、二进制路径、算例路径 app_name = CP2K
build_dir = /home/cp2k-8.2/
binary_dir = /home/CP2K/cp2k-8.2/bin/
case_dir = /home/CP2K/cp2k-8.2/benchmarks/QS/
[BUILD] HPC应用构建脚本 make -j 128
[CLEAN] HPC应用编译清理脚本 make -j 128 clean
[RUN] HPC应用运行配置,包括前置命令、应用命令和节点个数 run = mpirun -np 2
binary = cp2k.psmp H2O-256.inp
nodes = 1
[BATCH] HPC应用批量运行命令 #!/bin/bash
nvidia-smi -pm 1
nvidia-smi -ac 1215,1410
[PERF] 性能工具额外参数 perf= -o
nsys=
ncu=--target-processes all --launch-skip 71434 --launch-count 1

3.一键下载HPC应用(仅针对无需鉴权的链接,否则需要自行下载到downloads目录)

./jarvis -d

4.安装单个依赖

./jarvis -install [package/][name/version/other] [option]

option支持列表如下所示

选项值 解释 安装目录
gcc 使用当前gcc进行编译 software/libs/gcc
gcc+mpi 使用当前gcc+当前mpi进行编译 software/libs/gcc/mpi
clang 使用当前clang进行编译 software/libs/clang
clang+mpi 使用当前clang+当前mpi进行编译 software/libs/clang/mpi
bisheng 使用毕晟进行编译 software/libs/bisheng
bisheng+mpi 使用毕晟+当前mpi进行编译 software/libs/bisheng/mpi
nvc 使用当前nvc进行编译 software/libs/nvc
nvc+mpi 使用当前nvc+当前mpi进行编译 software/libs/nvc/mpi
icc 使用当前icc进行编译 software/libs/icc
icc+mpi 使用当前icc+当前mpi进行编译 software/libs/icc/mpi
com 安装编译器 software/compiler
any 安装工具软件 software/utils

注意,如果软件为MPI通信软件(如hmpi、openmpi),会安装到software/mpi目录

eg:

./jarvis -install bisheng/2.1.0 com   #安装毕晟编译器
./jarvis -install package/bisheng/2.1.0 com   #安装毕晟编译器
./jarvis -install fftw/3.3.8 gcc+mpi   #使用当前gcc和mpi编译fftw 3.3.8版本
./jarvis -install openmpi/4.1.2 gcc   #使用当前gcc编译openmpi 4.1.2版本

5.一键卸载依赖

./jarvis -remove openblas/0.3.18

6.一键下载并安装所有依赖(会读取配置文件中的[DEPENDENCY]字段内容并按顺序执行)

./jarvis -dp

7.输出已安装的软件清单

./jarvis -l

8.查询已安装的软件

./jarvis -f xxx

9.一键生成环境变量(会读取配置文件中的[ENV]字段内容并生成env.sh脚本执行,默认自动生成)

./jarvis -e && source ./env.sh

10.一键编译(会读取配置文件中的[BUILD]字段内容并生成build.sh脚本执行)

./jarvis -b

11.一键运行(会读取配置文件中的[RUN]字段内容并生成run.sh脚本执行)

./jarvis -r

12.一键性能采集(会读取配置文件中的[PERF]字段内容的perf值)

./jarvis -p

13.一键GPU性能采集(需安装nsys、ncu)

./jarvis -gp

14.一键输出服务器信息(包括CPU、网卡、OS、内存等)

./jarvis -i

15.一键服务器性能评测(包括MPI、OMP、P2P等)

./jarvis -bench all    #运行所有benchmark
./jarvis -bench mpi    #运行MPI benchmark
./jarvis -bench omp    #运行OMP benchmark
./jarvis -bench gemm   #运行矩阵运算 benchmark

16.切换配置(配置文件路径会保存到.meta文件中)

./jarvis -use XXX.config

17.根据当前配置生成Singularity容器定义文件

./jarvis -container docker-hub-address
eg: ./jarvis -container openeuler:openeuler

18.其它功能查看(网络检测等)

./jarvis -h

19.更新路径(如果移动了贾维斯的路径)

./jarvis -u

路标

RoadMap

欢迎贡献

贾维斯项目欢迎您的专业技能和热情参与!

小的改进或修复总是值得赞赏的;先从文档开始可能是一个很好的起点。如果您正在考虑做出更大贡献,请提交一个issue或者在hpc.openeuler.org进行讨论。

编写代码并不是为贾维斯做出贡献的唯一方法。您还可以:

  • 贡献安装脚本
  • 帮助我们测试新的HPC应用
  • 开发教程、演示
  • 为我们宣传
  • 帮助新的贡献者加入

请添加openEuler HPC SIG微信群了解更多HPC部署调优知识

微信群

技术文章

揭开HPC应用的神秘面纱:https://zhuanlan.zhihu.com/p/489828346

我和容器有个约会:https://zhuanlan.zhihu.com/p/499544308

贾维斯:完美而凛然HPC应用管家 https://zhuanlan.zhihu.com/p/518460349

木兰宽松许可证, 第2版 木兰宽松许可证, 第2版 2020年1月 http://license.coscl.org.cn/MulanPSL2 您对“软件”的复制、使用、修改及分发受木兰宽松许可证,第2版(“本许可证”)的如下条款的约束: 0. 定义 “软件”是指由“贡献”构成的许可在“本许可证”下的程序和相关文档的集合。 “贡献”是指由任一“贡献者”许可在“本许可证”下的受版权法保护的作品。 “贡献者”是指将受版权法保护的作品许可在“本许可证”下的自然人或“法人实体”。 “法人实体”是指提交贡献的机构及其“关联实体”。 “关联实体”是指,对“本许可证”下的行为方而言,控制、受控制或与其共同受控制的机构,此处的控制是指有受控方或共同受控方至少50%直接或间接的投票权、资金或其他有价证券。 1. 授予版权许可 每个“贡献者”根据“本许可证”授予您永久性的、全球性的、免费的、非独占的、不可撤销的版权许可,您可以复制、使用、修改、分发其“贡献”,不论修改与否。 2. 授予专利许可 每个“贡献者”根据“本许可证”授予您永久性的、全球性的、免费的、非独占的、不可撤销的(根据本条规定撤销除外)专利许可,供您制造、委托制造、使用、许诺销售、销售、进口其“贡献”或以其他方式转移其“贡献”。前述专利许可仅限于“贡献者”现在或将来拥有或控制的其“贡献”本身或其“贡献”与许可“贡献”时的“软件”结合而将必然会侵犯的专利权利要求,不包括对“贡献”的修改或包含“贡献”的其他结合。如果您或您的“关联实体”直接或间接地,就“软件”或其中的“贡献”对任何人发起专利侵权诉讼(包括反诉或交叉诉讼)或其他专利维权行动,指控其侵犯专利权,则“本许可证”授予您对“软件”的专利许可自您提起诉讼或发起维权行动之日终止。 3. 无商标许可 “本许可证”不提供对“贡献者”的商品名称、商标、服务标志或产品名称的商标许可,但您为满足第4条规定的声明义务而必须使用除外。 4. 分发限制 您可以在任何媒介中将“软件”以源程序形式或可执行形式重新分发,不论修改与否,但您必须向接收者提供“本许可证”的副本,并保留“软件”中的版权、商标、专利及免责声明。 5. 免责声明与责任限制 “软件”及其中的“贡献”在提供时不带任何明示或默示的担保。在任何情况下,“贡献者”或版权所有者不对任何人因使用“软件”或其中的“贡献”而引发的任何直接或间接损失承担责任,不论因何种原因导致或者基于何种法律理论,即使其曾被建议有此种损失的可能性。 6. 语言 “本许可证”以中英文双语表述,中英文版本具有同等法律效力。如果中英文版本存在任何冲突不一致,以中文版为准。 条款结束 如何将木兰宽松许可证,第2版,应用到您的软件 如果您希望将木兰宽松许可证,第2版,应用到您的新软件,为了方便接收者查阅,建议您完成如下三步: 1, 请您补充如下声明中的空白,包括软件名、软件的首次发表年份以及您作为版权人的名字; 2, 请您在软件包的一级目录下创建以“LICENSE”为名的文件,将整个许可证文本放入该文件中; 3, 请将如下声明文本放入每个源文件的头部注释中。 Copyright (c) [Year] [name of copyright holder] [Software Name] is licensed under Mulan PSL v2. You can use this software according to the terms and conditions of the Mulan PSL v2. You may obtain a copy of Mulan PSL v2 at: http://license.coscl.org.cn/MulanPSL2 THIS SOFTWARE IS PROVIDED ON AN "AS IS" BASIS, WITHOUT WARRANTIES OF ANY KIND, EITHER EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO NON-INFRINGEMENT, MERCHANTABILITY OR FIT FOR A PARTICULAR PURPOSE. See the Mulan PSL v2 for more details. Mulan Permissive Software License,Version 2 Mulan Permissive Software License,Version 2 (Mulan PSL v2) January 2020 http://license.coscl.org.cn/MulanPSL2 Your reproduction, use, modification and distribution of the Software shall be subject to Mulan PSL v2 (this License) with the following terms and conditions: 0. Definition Software means the program and related documents which are licensed under this License and comprise all Contribution(s). Contribution means the copyrightable work licensed by a particular Contributor under this License. Contributor means the Individual or Legal Entity who licenses its copyrightable work under this License. Legal Entity means the entity making a Contribution and all its Affiliates. Affiliates means entities that control, are controlled by, or are under common control with the acting entity under this License, ‘control’ means direct or indirect ownership of at least fifty percent (50%) of the voting power, capital or other securities of controlled or commonly controlled entity. 1. Grant of Copyright License Subject to the terms and conditions of this License, each Contributor hereby grants to you a perpetual, worldwide, royalty-free, non-exclusive, irrevocable copyright license to reproduce, use, modify, or distribute its Contribution, with modification or not. 2. Grant of Patent License Subject to the terms and conditions of this License, each Contributor hereby grants to you a perpetual, worldwide, royalty-free, non-exclusive, irrevocable (except for revocation under this Section) patent license to make, have made, use, offer for sale, sell, import or otherwise transfer its Contribution, where such patent license is only limited to the patent claims owned or controlled by such Contributor now or in future which will be necessarily infringed by its Contribution alone, or by combination of the Contribution with the Software to which the Contribution was contributed. The patent license shall not apply to any modification of the Contribution, and any other combination which includes the Contribution. If you or your Affiliates directly or indirectly institute patent litigation (including a cross claim or counterclaim in a litigation) or other patent enforcement activities against any individual or entity by alleging that the Software or any Contribution in it infringes patents, then any patent license granted to you under this License for the Software shall terminate as of the date such litigation or activity is filed or taken. 3. No Trademark License No trademark license is granted to use the trade names, trademarks, service marks, or product names of Contributor, except as required to fulfill notice requirements in Section 4. 4. Distribution Restriction You may distribute the Software in any medium with or without modification, whether in source or executable forms, provided that you provide recipients with a copy of this License and retain copyright, patent, trademark and disclaimer statements in the Software. 5. Disclaimer of Warranty and Limitation of Liability THE SOFTWARE AND CONTRIBUTION IN IT ARE PROVIDED WITHOUT WARRANTIES OF ANY KIND, EITHER EXPRESS OR IMPLIED. IN NO EVENT SHALL ANY CONTRIBUTOR OR COPYRIGHT HOLDER BE LIABLE TO YOU FOR ANY DAMAGES, INCLUDING, BUT NOT LIMITED TO ANY DIRECT, OR INDIRECT, SPECIAL OR CONSEQUENTIAL DAMAGES ARISING FROM YOUR USE OR INABILITY TO USE THE SOFTWARE OR THE CONTRIBUTION IN IT, NO MATTER HOW IT’S CAUSED OR BASED ON WHICH LEGAL THEORY, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. 6. Language THIS LICENSE IS WRITTEN IN BOTH CHINESE AND ENGLISH, AND THE CHINESE VERSION AND ENGLISH VERSION SHALL HAVE THE SAME LEGAL EFFECT. IN THE CASE OF DIVERGENCE BETWEEN THE CHINESE AND ENGLISH VERSIONS, THE CHINESE VERSION SHALL PREVAIL. END OF THE TERMS AND CONDITIONS How to Apply the Mulan Permissive Software License,Version 2 (Mulan PSL v2) to Your Software To apply the Mulan PSL v2 to your work, for easy identification by recipients, you are suggested to complete following three steps: i Fill in the blanks in following statement, including insert your software name, the year of the first publication of your software, and your name identified as the copyright owner; ii Create a file named “LICENSE” which contains the whole context of this License in the first directory of your software package; iii Attach the statement to the appropriate annotated syntax at the beginning of each source file. Copyright (c) [Year] [name of copyright holder] [Software Name] is licensed under Mulan PSL v2. You can use this software according to the terms and conditions of the Mulan PSL v2. You may obtain a copy of Mulan PSL v2 at: http://license.coscl.org.cn/MulanPSL2 THIS SOFTWARE IS PROVIDED ON AN "AS IS" BASIS, WITHOUT WARRANTIES OF ANY KIND, EITHER EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO NON-INFRINGEMENT, MERCHANTABILITY OR FIT FOR A PARTICULAR PURPOSE. See the Mulan PSL v2 for more details.

简介

openEuler High Performance Computing(HPC) Runner, provides universal portal for hpc users and developers. 展开 收起
MulanPSL-2.0
取消

发行版

暂无发行版

贡献者

全部

近期动态

加载更多
不能加载更多了
1
https://gitee.com/shaoyuteng/hpcrunner.git
git@gitee.com:shaoyuteng/hpcrunner.git
shaoyuteng
hpcrunner
hpcrunner
master

搜索帮助