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Installation Guide for Codes and Libraries

First of all! Load the environments!

Before you install anything, especially when you need to compile codes, make sure the type of compiler and the version of compiler you have. Usually, in your personal computer, you can use compiler command directly, for instance, gcc, gfortran, ifort,mpic++. In remote cluster(High Performance Cluster), the compiler is managed by module. You cannnot use it unless you load it in advance. Therefore, make sure which compiler you have in module, and use command such as module load gcc/4.9.4 to load required compilers.

General Protocal for Installation:

  1. Compile the Code
  2. Quick test the code at server node
  3. Write module files to code (we recommend to manage codes by module)
  4. Test the code in the client node
  5. write example lsf file in /share/base/scripts

Where to Install?

Install in the /share/ directory. /share/ directory is the one synchronized to all the nodes by nfs.

  1. Libraries: /share/apps/lib/<library name>/<version>
  2. Codes, Pacakges, Softwares: /share/apps/<packages name>/<version>

Standard in Writing Module file

  1. module name: <package name>/<version>, like cp2k/6.1

Standard in Writing lsf file

  1. export necessary environmental variable
  2. load prerequisite module

Anaconda Installation Guide

Short Introduction

The open-source Anaconda Distribution is the easiest way to perform Python/R data science and machine learning on Linux, Windows, and Mac OS X. Choose the one suitable for you usage. If you'd like to use Anaconda in Cluster, ask cluster administrator if Anaconda have been installed, which avoid storage waste in your cluster's storage.

Tip

A minimum version of Conda is install in cluster51 by Yunpei Liu. Use it by module command

Installation Guide

  • Go to this website, choose the right version for you. Personally, I recommend command line Installer for Linux and Mac OS System, while the Graphical Installer for Windows System
  • Follow the instruction in this page

QUIP Installation Guide

Short Introduction

The QUIP package is a collection of software tools to carry out molecular dynamics simulations. It implements a variety of interatomic potentials and tight binding quantum mechanics, and is also able to call external packages, and serve as plugins to other software such as LAMMPS, CP2K and also the python framework ASE. Various hybrid combinations are also supported in the style of QM/MM, with a particular focus on materials systems such as metals and semiconductors.

Tip

The tested compiler version: and for your information.

Use QUIP and quippy in cluster 51

If you need use QUIP/GAP in cluster 51, please used command: 

module load gcc/6.3.0 mpi/openmpi/3.0.0
module load QUIP/GAP

If you want to use quippy:

module load miniconda/3
source activate /share/apps/QUIP/quippy-py3/

Install Guide

  • Git clone from repository
git clone --recursive https://github.com/libAtoms/QUIP.git
  • Go to the package root and export variable
export QUIP_ARCH=linux_x86_64_gfortran
  • Make configuration
make config
#if everything fine
make

Packages and Extra Interfaces of QUIP

Add GAP Packages

  • Download GAP file from here, then you obtain a tar file named GAP.tar, unzip it
tar -xvf GAP.tar
  • You will obtain a directory named GAP/, copy this directory into QUIP root/src.
cp -r GAP <QUIP root>/src/
  • Reconfig your make by choose install GAP as y 
#recompile this code again
make

Build QUIPPY, A QUIP Python Interface

  • Export another environmental variable
#install for your self
export QUIPPY_INSTALL_OPTS=--user
#choose the location for installation of quippy
export QUIPPY_INSTALL_OPTS=--prefix=<directory>
  • Go to <QUIP root>/src/f90wrap, and install f90wrap by:
pip install .
  • Back to <QUIP root>
make install-quippy
  • Test whether installed successfully.
make test

Trouble Shooting

ImportError: dynamic module does not define module export function
Example:
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/share/apps/QUIP/quippy-py3/lib/python3.8/site-packages/quippy-https_github.com_libAtoms_QUIP.git_ec1ed34_dirty-py3.8-linux-x86_64.egg/quippy/__init__.py", line 2, in <module>
    import _quippy
ImportError: dynamic module does not define module export function (PyInit__quippy)

Solution: add /build/${QUIP_ARCH} into your Python PATH

VASP

Short Introduction

(TODO)

Install Guide

  1. Get the VASP source code and pseudopotentials.

  2. Load environment 

    module load intel

  3. Choose makefile.include according to the platform and make 

    cd vasp.5.4.4
make std
make gam

  4. If everything is right, you will find vasp_std in vasp.5.4.4/build/std and you can run it with mpirun -np 24 vasp_std.

Plugins

Wannier90

  1. Download Wannier90 from http://www.wannier.org/download/ . Notice: currently VASP only support Wannier90-1.2

  2. Modify compile file for Wannier90 make.sys.intel. Here we use the MKL. 

    #LIBDIR = /opt/intel/mkl721/lib/32
#LIBS = -L$(LIBDIR) -lmkl_lapack -lmkl_ia32 -lguide -lpthread
LIBDIR = $(MKLROOT)/lib/intel64
LIBS = -L$(LIBDIR) -mkl -lpthread

  3. Compile and test 

    cp ./config/make.inc.ifort make.inc
make 
make lib # compile to get the libary: libwannier.a 
make tests # test whether the compilation is success

  4. Copy the libwannier.a libary file to VASP libary path and modify VASP makefile.include.

#Precompiler options
CPP_OPTIONS= -DHOST=\"LinuxIFC\"\
             -DMPI -DMPI_BLOCK=8000 \
             -Duse_collective \
             -DscaLAPACK \
             -DCACHE_SIZE=4000 \
             -Davoidalloc \
             -Duse_bse_te \
             -Dtbdyn \
             -Duse_shmem \
             -DVASP2WANNIER90   ## modify this line for Wannier90

LLIBS += ../../libwannier.a  ## change here to the location of libwannier.a

Compilation optimization

If you use Intel Xeon Silver/Gold/Platium CPU, using the following compilation parameters will get a 2✖ speedup! (Already test on 205 server) 

OFLAG      = -O3 -xCORE-AVX512

TODO in the future

  1. Install vasp_gpu version
  2. Benchmark different libary (FFTW/MKL)
  3. other plugins: VASP-neb, vasp-beef
  4. vasp6

LAMMPS Installation Guide

Short Introduction

LAMMPS is a classical molecular dynamics code with a focus on materials modeling. It's an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator.

Tip

I have installed one in cluster51, in directory /share/apps/lammps-7Aug19/. The compiler version: and for your information.

Install Guide

  • Git clone or download package from website
# command for git
git clone -b stable https://github.com/lammps/lammps.git mylammps
  • We assume you the package path is 
cd <lammps-root>/src
#choose one of the following or both
# build a serial LAMMPS executable
make serial 
# build a parallel LAMMPS executable with MPI
make mpi
  • You will see the executable binary in src/lmp_serial or src/lmp_mpi

Packages and Extra Interfaces of LAMMPS

Tip

Contact Cluster Administrator if you need any uninstalled packages

General for Installing Package

  • To install package of LAMMPS, just type make yes-<package name> for example, make yes-user-intel

Building USER-ATC Package

  • Before you install this package by make yes-user-atc, you should install lib-atc which is a library for atc package
  • Go to the directory <LAMMPS root>/lib/atc, you can follow the instruction in the README. Remember to load module gcc and open mpi
cd <LAMMPS root>/lib/atc
  • lib-atc need library lapack and blas installed. Check whether this library installed or not by command:
#check for lapack library
ldconfig -p | grep lapack
#check for blas library
ldconfig -p | grep blas
  • If lapack and blas are installed. Change the value of EXTRAMAKE variable to Makefile.lammps.installed in the file Makefile.mpi.
EXTRAMAKE= Makefile.lammps.installed
  • Make library by following command
make -f Makefile.mpi
  • Make sure you have libatc.a and Makefile.lammps in your current directory
  • Back to directory <LAMMPS root>/src/ and type make mpi to compile mpi version of LAMMPS

Building Inteface with n2p2

  • make sure you have shared library libnnpif-shared in your <path to n2p2>/lib/
  • export the following in your environmental variable(optional)
#export this if you use shared library, skip if you are using static library
export LD_LIBRARY_PATH=<path to n2p2>/lib:${LD_LIBRARY_PATH}
  • Go to LAMMPS root
cd <LAMMPS root>/
ln -s <path to n2p2> lib/nnp
cp -r <path to n2p2>/src/interface/LAMMPS/src/USER-NNP <LAMMPS root>/src
cd <LAMMPS root>/src
make yes-user-nnp
make mpi

Building with Plumed

  • Before you install, make sure the Plumed has installed
  • To directory <LAMMPS root>/src/ 
make lib-plumed args="-p <path to plumed directory>"
make yes-user-plumed
make mpi

DeePMD Installation Guide

Short Introduction

DeePMD-kit is a package written in Python/C++, designed to minimize the effort required to build deep learning based model of interatomic potential energy and force field and to perform molecular dynamics (MD). This brings new hopes to addressing the accuracy-versus-efficiency dilemma in molecular simulations. Applications of DeePMD-kit span from finite molecules to extended systems and from metallic systems to chemically bonded systems. Ref. Paper

Install Guide

  • Here, we display the most easiest way to install DeePMD Code.
  • Make sure you have GPU install in your computer. Usually, you can check with the drive of GPU
  • Install the anaconda3 from website. After you installed anaconda3, you can use conda command.
  • Install DeePMD with cpu or gpu version. Installation by this way will install lammps as well.
#install of cpu version
conda install deepmd-kit=*=*cpu lammps-dp=*=*cpu -c deepmodeling
#install of gpu version
conda install deepmd-kit=*=*gpu lammps-dp=*=*gpu -c deepmodeling
  • That's all for installation. Check the install package use command:
conda list | grep deep
  • You will find four packages related with DeePMD code. You can now directly use command dp , lmp.
  • To test DeePMD Code. Download DeePMD code from github by:
git clone https://github.com/deepmodeling/deepmd-kit.git
  • Go to the directory examples/water/train/
  • Test training by
dp train water_se_a.json

Install Guide of DeePMD

快速安装

n2p2 Installation Guide

Short Introduction

n2p2 is a machine learning code to training a machine learning potential. It original paper is from J. Behler and M. Parrinello, Phys. Rev. Lett. 98, 146401 (2007)

Install Guide

  • Before Installation, make sure you have installed the Eigen Library and the GSL Library.
  • Make sure you have gcc compiler (including gfortran), I haven't successfully compiled by intel compiler. Make sure you have open MPI(i. e. for mpic++ command).
  • Download the n2p2 code from github: https://github.com/CompPhysVienna/n2p2. For example, using the following command.
git clone https://github.com/CompPhysVienna/n2p2.git
  • You can see a directory named n2p2, now go into that by:
cd n2p2/src
  • Modify the configure file makefile.gnu 
#modify this file, I just pick out the part you need to modify
# Enter here paths to GSL or EIGEN if they are not in your standard include
# path. DO NOT completely remove the entry, leave at least "./".
PROJECT_GSL=<path to gsllib>/gsl/include/ # substitute <path> with real path
PROJECT_EIGEN=<path to eigen>/eigen-eigen-323c052e1731 # substitute <path> with real path

 ###############################################################################
 # COMPILERS AND FLAGS
 ###############################################################################
PROJECT_CFLAGS=-O3 -march=native -std=c++11 -fopenmp -L<pato to gsllib>gsl/lib
PROJECT_LDFLAGS_BLAS=-lblas -lgslcblas
  • Save and quit this file, use the following command to compile code:
#choose one of the following command
make MODE=shared # compile a binary with shared library
make MODE=static # compile a binary with static library, I use this one
  • After you compiled successfully, you will have all the excutable binary at n2p2/bin/ directory
  • Add n2p2/bin/ to your PATH environmental variable, you can easily use this. The most important binary is nnp-train, this is used for training.
  • Add n2p2 library to your LD_LIBRARY_PATH in .bashrc
export LD_LIBRARY_PATH=<Path to n2p2>/lib/:$LD_LIBRARY_PATH

Plumed Installation Guide

Short Introduction

PLUMED is an open-source, community-developed library that provides a wide range of different methods, which include:

  • enhanced-sampling algorithms
  • free-energy methods
  • tools to analyze the vast amounts of data produced by molecular dynamics (MD) simulations.

These techniques can be used in combination with a large toolbox of collective variables that describe complex processes in physics, chemistry, material science, and biology.

Tip

I have installed one in cluster51. Use module load plumed/2.6.0 to use this library. The compiler version: for your information

Install Guide

  • Download package from here.
  • Basic Configure
./configure --prefix=<path you want to install> LDFLAGS=-L'/share/apps/lib/fftw/3.3.8/lib' CPPFLAGS=-I'/share/apps/lib/fftw/3.3.8/lib '
  • Compile
make -j 32
make install

Eigen Library Installation Guide

Short Introduction

Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.

Install Guide

  • Download the package from wiki:http://eigen.tuxfamily.org/index.php?title=Main_Page#Overview. For me, I choose the Eigen 3.3.7 released version.
wget http://bitbucket.org/eigen/eigen/get/3.3.7.tar.bz2
  • Unpack this tar file by 
tar -zxvf 3.3.7.tar.gz
  • You will have eigen-eigen-* directory in your computer
  • These are all steps you need to install eigen library

GSL Library Installation Guide

Short Introduction

The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. It is a free open source library under the GNU General Public License.

This guide is from: website tutorial

Tip

I have installed one in cluster51, in directory /share/apps/lib/gsl-2.6. The compiler version: for your information

Install Guide

wget ftp://ftp.gnu.org/gnu/gsl/gsl-latest.tar.gz
  • Place the file in whatever directory you want to install and unpack the file with the following command:
tar -zxvf gsl-latest.tar.gz
  • This will create a directory called gsl-*.* in your home directory. Change to this directory.
cd gsl-*.*
  • The next step is to configure the installation and tell the system where to install the files. Create a directory to install your gsl package, say <Path to libgsl>/gsl with the following command
mkdir <Path to libgsl>/gsl
  • Now configure the installation and tell it to use your new directory. This step may take a few minutes.
./configure --prefix=<Path to libgsl>/gsl
  • If there are no errors, compile the library. This step will take several minutes.
make
  • Now it is necessary to check and test the library before actually installing it. This step will take some time.
make check
  • If there are no errors, go ahead and install the library with:
make install
  • Now we can write a test program to see if the library works. Create the following program and name it example.c
#include <stdio.h>
#include <gsl/gsl_sf_bessel.h>

int
main (void)
{
    double x = 15.0;
    double y = gsl_sf_bessel_J0 (x);
    printf ("J0(%g) = %.18e/n", x, y);
    return 0;
}
  • Compile and link the program with the following commands (but use the correct path for your username):
gcc -Wall -I<Path to libgsl>/gsl/include -c example.c
gcc -L<Path to libgsl>/gsl/lib example.o -lgsl -lgslcblas -lm
  • Now run your program!
./a.out
  • If it is succesfully installed, it will print a number in your screen.
  • add libray path to LD_LIBRARY_PATH in .bashrc
export LD_LIBRARY_PATH=<path to libgsl>/lib:$LD_LIBRARY_PATH

Libxc Library Installation Guide

  • Download the latest stable version of libxc from official website:
wget http://www.tddft.org/programs/libxc/down.php?file=4.3.4/libxc-4.3.4.tar.gz

FFTW Library Installation Guide

Short Introduction

FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data (as well as of even/odd data, i.e. the discrete cosine/sine transforms or DCT/DST).

Tip

I have installed one in cluster51, in directory /share/apps/lib/fftw/3.3.8. Use module load fftw/3.3.8 to use this library. The compiler version: for your information

Install Guide

  • Download the release version from official website using wget
wget http://www.fftw.org/fftw-3.3.8.tar.gz
  • Unzi the package
tar -xvf fftw-3.3.8.tar.gz
  • Go to the directory fftw-3.3.8
./configure --prefix=<path to you want to install>    \
            --enable-shared  \
            --enable-threads \
            --enable-sse2    \
            --enable-avx
  • If configure is finished
make
#check if you install finished
make check
#install to the final directory which you have set in --prefix
make install

CP2K Installation Guide

  • Download the release version from official website using wget like
wget https://github.com/cp2k/cp2k/releases/download/v6.1.0/cp2k-6.1.tar.bz2
  • Unzip the cp2k package
tar -xvf cp2k-6.1.tar.bz2
  • Go into directory cp2k-6.1/tools/toolchains/
  • Stop here! you should check you compiler version, if you are in the High Performance Cluster, Please load the module for compiler and MPI/Open MPI
  • Note: for gcc version, gcc <= 7.4.0
  • Execute the following script to see the help message
./install_cp2k_toolchain.sh -h
  • Choose which package you want to install before cp2k.

Some packages are essential for cp2k, please check this in the official web site

  • the minimum required is with-openblas=install, if you want to compile successfully.

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