Xushan Zhao, Yang Chen

Application of ab initio

In Zr-alloys for Nuclear

Power Stations

General Research Institute for Non-Ferrous metals of Beijing September 2010

Zr-alloys : Safety Wall of Nuclear Station

Characteristics:• Low neutron absorption

Cross section • High strength • Good ductility• Low corrosion rate

Main Purposes:• Nuclear reactor fuel cladding

PROPERTY

COMPOSITION STUCTURE

Our Application

PR

ED

IC

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Our Application and Expectation

Softpackage

A package for performing ab-initio quantum-mechanical molecular dynamics (MD) .

Installation of the Program

1. Fortran Compiler compile the Vasp software

2. Math Kernel Library used during the calculation

3. Install MPICH2 for parallel calculation

First Step: Install the Fortran Compiler

unpack it into a writeable directory of your choice using the command:

tar –xzvf name-of-downloaded-file

change the directory (cd) to the directory containing the unpacked files and begin the installation using the command:

./install.sh

Establishing the Compiler Environment :source

/opt/intel/Compiler/11.1/xxx/bin/ifortvars.sh (default for system-wide installation is /opt/intel)

free tools for non-commercial software development

Second Step: Install Math Kernel Library

Intel® Math Kernel Library (Intel® MKL) is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more. Offering performance optimizations for current and next-generation Intel® processors, it includes improved integration with Microsoft Visual Studio*, Eclipse*, and XCode*.

free tools for non-commercial software development

change the directory (cd) to the directory containing the unpacked files and begin the installation using the command:

./install.sh

Third Step: Install MPICH2

Unpack the tar file and go to the top level directory:

tar xzf mpich2-1.3b1.tar.gzcd mpich2-1.3b1

Configure MPICH2 specifying the installation directory:

./configure --prefix=/home/<USERNAME>/mpich2-install

Then:make

make install

Final Step: Install Our Program

There are two directories in which VASP resides:• …/vasp.5.lib holds files which change rarely, but might require considerable

changes for supporting new machines• …/vasp.5.2 contains the VASP code, and changes with every update.

cd vasp.4.libcp makefile.machine makefile

You might choose makefile.machine from the following list: makefile.cray makefile.dec makefile.hp makefile.linux_abs makefile.linux_alpha makefile.linux_ifc_P4 makefile.linux_ifc_ath makefile.linux_pg makefile.nec makefile.rs6000 makefile.sgi makefile.sp2 makefile.sun makefile.t3d makefile.t3e makefile.vpp

mpif90

Modify the makefile in vasp.lib directory

Thenmake

we will obtain a libdmy.a file

In vasp.5.2 directory:

Modify the directory of MKL libraryThen &make , we will obtain the vasp excutive file.

How VASP runs?MPI Version of VASP:It generates several MPI processes on each core and parallel execution between nodes , is performed using MPI communication between processes.

Generate several mpi processers

WN1

WN2

WN3

WN4

WN5

WN6

WN7

……………..

Submit job to the WN

4 Input files

mpdbootmpirun -np 2 vasp >&runlog

runlog files

Onput files

input files<1 Mb

output files<100 Mb

.pbs FILE ………..########################################### Output some useful job information. ########################################## JOBINFOR=$PBS_JOBIDMASTERNODE=`hostname`SCRATCHDIR=$PBS_JOBIDNCPU=`wc -l < $PBS_NODEFILE` SERVER=$PBS_O_HOSTWORKDIR=$PBS_O_WORKDIRMKDIR=/bin/mkdirRSH=/usr/bin/rshCP=/bin/cpLAUNCH="/disk6/xlxy50123k/copy/mpich-1.2.7p1/bin/mpirun -np $NCPU -machinefile “ location of mpich and the number of CPUS We NeededPROGRAMEXEC="/disk6/xlxy50123k/copy/bin/vasp.neb“ calling VASP program…….

To run the job :qsub vasp.pbs -l nodes=20:ppn=1 -N job

Some Information Of the test job:

Our Demand on CPU’s

• One Single run:• 20~30*3.06G Intel Xeon CPU， 2GB Memory• Cost: 2-7 days depend on the accuracy we set • One simulation always have >10 jobs

• Therefore:• ~100 CPU’S maybe enough for our job • More CPU’s will help us to reach high accuracy