CentOS 7 环境安装Lammps，VASP等软件
CentOS 7 环境安装Lammps，VASP等软件
一、编译环境
使用CentOS 7 和 Intel oneAPI 2021
- 安装基础的开发工具包，需要
root权限，一般用于计算的工作站都已经包含了这些软件
sudo yum -y update
sudo yum -y install wget cmake pkgconfig
sudo yum -y groupinstall "Development Tools"
- 下载和安装Intel® oneAPI Base Toolkit、Intel® oneAPI HPC Toolkit，其实也就是以前的
Intel Parallel Studio XE，如果下载较慢可以先用迅雷下载再运行，注意磁盘空间，下载需要 3.5 GB，安装需要 23.3 GB。
wget -c https://registrationcenter-download.intel.com/akdlm/irc_nas/17431/l_BaseKit_p_2021.1.0.2659_offline.sh
wget -c https://registrationcenter-download.intel.com/akdlm/irc_nas/17427/l_HPCKit_p_2021.1.0.2684_offline.sh
sh l_BaseKit_p_2021.1.0.2659_offline.sh -f /tmp -s -a --silent --eula accept
sh l_HPCKit_p_2021.1.0.2684_offline.sh -f /tmp -s -a --silent --eula accept
使用普通用户将会安装到$HOME/intel/oneapi目录，使用root用户将会安装到/opt/intel/oneapi目录，使用普通用户即可，安装完成可以看到如下目录结构
[vagrant@localhost oneapi]$ pwd
/home/vagrant/intel/oneapi
[vagrant@localhost oneapi]$ tree -L 1
.
├── advisor
├── ccl
├── clck
├── common.sh
├── compiler
├── conda_channel
├── dal
├── debugger
├── dev-utilities
├── dnnl
├── dpcpp-ct
├── dpl
├── etc
├── inspector
├── installer
├── intelpython
├── ipp
├── ippcp
├── itac
├── licensing
├── logs
├── mkl
├── modulefiles-setup.sh
├── mpi
├── readme-get-started-linux-base-kit.html
├── readme-get-started-linux-hpc-kit.html
├── setvars.sh
├── support.txt
├── sys_check.sh
├── tbb
├── vpl
└── vtune
25 directories, 7 files
二、Lammps
LAMMPS即Large-scale Atomic/Molecular Massively Parallel Simulator，可以翻译为大规模原子分子并行模拟器，主要用于分子动力学相关的一些计算和模拟工作。
cd $HOME && source ~/intel/oneapi/setvars.sh
wget -c https://github.com/lammps/lammps/archive/stable_29Oct2020.tar.gz && tar xvf stable_29Oct2020.tar.gz && cd lammps-stable_29Oct2020/src
make yes-USER-REAXC
make intel_cpu_intelmpi -j8
Benchmark
## benchmark
cd $HOME/lammps-stable_29Oct2020/bench && mpirun -np 16 ../src/lmp_intel_cpu_intelmpi -var x 2 -var y 2 -var z 4 -in in.lj
cd $HOME/lammps-stable_29Oct2020/examples/reax && mpirun -np 16 ../../src/lmp_intel_cpu_intelmpi -in in.reaxc.rdx
三、VASP
VASP是维也纳大学Hafner小组开发的进行电子结构计算和量子力学-分子动力学模拟软件包。它是目前材料模拟和计算物质科学研究中最流行的商用软件之一。
cd $HOME && source ~/intel/oneapi/setvars.sh
wget -c http://img3.betajie.com/scikit/vasp.5.4.1.24Jun15.tar.gz && tar xvf vasp.5.4.1.24Jun15.tar.gz && cd vasp.5.4.1
cp arch/makefile.include.linux_intel makefile.include
sed -i -e 's/= mpif90/= mpiifort/g' makefile.include
sed -i -e 's/-lmkl_blacs_openmpi_lp64/-lmkl_blacs_intelmpi_lp64/g' makefile.include
if [ ! -f $MKLROOT/interfaces/fftw3xf/libfftw3xf_intel.a ]; then
cp -r $MKLROOT/interfaces/fftw3xf $HOME && cd $HOME/fftw3xf && make libintel64
cd $HOME/vasp.5.4.1 && sed -i -e 's/$(MKLROOT)/interfaces/fftw3xf/libfftw3xf_intel.a/$(HOME)/fftw3xf/libfftw3xf_intel.a/g' makefile.include
fi
make veryclean
# !!! VASP makefile is not support multiprocessor compiler, do not add -j flag
make all
ls -alh bin
Benchmark
wget -c https://www.vasp.at/wiki/images/1/19/H2o_on_tio2.tgz && tar xvf H2o_on_tio2.tgz && cd h2o_on_tio2/constrMD_microcanonical
mpirun -genv I_MPI_DEBUG 5 -np 8 -ppn 1 -host localhost ~/vasp.5.4.1/bin/vasp_std
[vagrant@localhost constrMD_microcanonical]$ mpirun -genv I_MPI_DEBUG 5 -np 8 -ppn 1 -host localhost ~/vasp.5.4.1/bin/vasp_std
[0] MPI startup(): Intel(R) MPI Library, Version 2021.1 Build 20201112 (id: b9c9d2fc5)
[0] MPI startup(): Copyright (C) 2003-2020 Intel Corporation. All rights reserved.
[0] MPI startup(): library kind: release
[0] MPI startup(): libfabric version: 1.11.0-impi
[0] MPI startup(): libfabric provider: tcp;ofi_rxm
[0] MPI startup(): Rank Pid Node name Pin cpu
[0] MPI startup(): 0 21638 localhost.localdomain 0
[0] MPI startup(): 1 21639 localhost.localdomain 1
[0] MPI startup(): 2 21640 localhost.localdomain 2
[0] MPI startup(): 3 21641 localhost.localdomain 3
[0] MPI startup(): 4 21642 localhost.localdomain 0
[0] MPI startup(): 5 21643 localhost.localdomain 1
[0] MPI startup(): 6 21644 localhost.localdomain 2
[0] MPI startup(): 7 21645 localhost.localdomain 3
[0] MPI startup(): I_MPI_ROOT=/home/vagrant/intel/oneapi/mpi/2021.1.1
[0] MPI startup(): I_MPI_MPIRUN=mpirun
[0] MPI startup(): I_MPI_HYDRA_TOPOLIB=hwloc
[0] MPI startup(): I_MPI_INTERNAL_MEM_POLICY=default
[0] MPI startup(): I_MPI_DEBUG=5
running on 8 total cores
distrk: each k-point on 8 cores, 1 groups
distr: one band on 1 cores, 8 groups
using from now: INCAR
vasp.5.4.1 24Jun15 (build Jan 14 2021 01:54:48) complex
POSCAR found type information on POSCAR Ti O H
POSCAR found : 3 types and 9 ions
scaLAPACK will be used
-----------------------------------------------------------------------------
| |
| W W AA RRRRR N N II N N GGGG !!! |
| W W A A R R NN N II NN N G G !!! |
| W W A A R R N N N II N N N G !!! |
| W WW W AAAAAA RRRRR N N N II N N N G GGG ! |
| WW WW A A R R N NN II N NN G G |
| W W A A R R N N II N N GGGG !!! |
| |
| For optimal performance we recommend to set |
| NCORE= 4 - approx SQRT( number of cores) |
| NCORE specifies how many cores store one orbital (NPAR=cpu/NCORE). |
| This setting can greatly improve the performance of VASP for DFT. |
| The default, NPAR=number of cores might be grossly inefficient |
| on modern multi-core architectures or massively parallel machines. |
| Do your own testing !!!! |
| Unfortunately you need to use the default for GW and RPA calculations. |
| (for HF NCORE is supported but not extensively tested yet) |
| |
-----------------------------------------------------------------------------
LDA part: xc-table for Pade appr. of Perdew
-----------------------------------------------------------------------------
| |
| W W AA RRRRR N N II N N GGGG !!! |
| W W A A R R NN N II NN N G G !!! |
| W W A A R R N N N II N N N G !!! |
| W WW W AAAAAA RRRRR N N N II N N N G GGG ! |
| WW WW A A R R N NN II N NN G G |
| W W A A R R N N II N N GGGG !!! |
| |
| VASP found 18 degrees of freedom |
| the temperature will equal 2*E(kin)/ (degrees of freedom) |
| this differs from previous releases, where T was 2*E(kin)/(3 NIONS). |
| The new definition is more consistent |
| |
-----------------------------------------------------------------------------
POSCAR, INCAR and KPOINTS ok, starting setup
WARNING: small aliasing (wrap around) errors must be expected
FFT: planning ...
WAVECAR not read
prediction of wavefunctions initialized - no I/O
entering main loop
N E dE d eps ncg rms rms(c)
DAV: 1 0.365928404142E+03 0.36593E+03 -0.13247E+04 832 0.808E+02
DAV: 2 -0.471497687791E+01 -0.37064E+03 -0.35445E+03 1304 0.218E+02
DAV: 3 -0.835496235250E+02 -0.78835E+02 -0.78061E+02 1040 0.124E+02
DAV: 4 -0.857147612524E+02 -0.21651E+01 -0.21637E+01 920 0.271E+01
DAV: 5 -0.857782211221E+02 -0.63460E-01 -0.63451E-01 1120 0.436E+00 0.347E+01
DAV: 6 -0.676314972968E+02 0.18147E+02 -0.13418E+02 1216 0.547E+01 0.300E+01
DAV: 7 -0.679648482636E+02 -0.33335E+00 -0.15612E+02 1288 0.762E+01 0.168E+01
