GRINM-Presentation

Report
Application of ab initio
In Zr-alloys for Nuclear
Power Stations
Xushan Zhao, Yang Chen
General Research Institute for NonFerrous 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
Our Application and Expectation
PROPERTY
PREDICT
COMPOSITION
STUCTURE
Our Application
Softpackage
 A package for performing ab-initio quantum-mechanical molecular dynamics
(MD) .
Installation of the Program
1. Fortran Compiler
2. Math Kernel Library
3. Install MPICH2
compile the Vasp software
used during the calculation
for parallel calculation
First Step: Install the Fortran Compiler
free tools for non-commercial software development
 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)
Second Step: Install Math Kernel Library
free tools for non-commercial software development
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*.
 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.gz
cd 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.lib
cp 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
Modify the makefile in vasp.lib directory
mpif90
Then
make
we will obtain a libdmy.a file
In vasp.5.2 directory:
Modify the directory of MKL library
Then &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
Submit job to the WN
WN
1
WN
2
WN
3
WN
4
WN
5
WN
6
WN
7
……………..
4 Input files
mpdboot
mpirun -np 2 vasp >&runlog
runlog files
Onput files
input files
<1 Mb
output files
<100 Mb
.pbs FILE
………..
##########################################
# Output some useful job information.
##########################################
JOBINFOR=$PBS_JOBID
MASTERNODE=`hostname`
SCRATCHDIR=$PBS_JOBID
NCPU=`wc -l < $PBS_NODEFILE`
SERVER=$PBS_O_HOST
WORKDIR=$PBS_O_WORKDIR
MKDIR=/bin/mkdir
RSH=/usr/bin/rsh
CP=/bin/cp
LAUNCH="/disk6/xlxy50123k/copy/mpich-1.2.7p1/bin/mpirun -np $NCPU machinefile “
location of mpich and the number of CPUS We Needed
PROGRAMEXEC="/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

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