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
Dec 22, 2015
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
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
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
.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