Difference between revisions of "HPC VASP"

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(Created page with "'''none''' '''The Vienna Ab initio Simulation Package (VASP''') is a computer program for atomic scale materials modelling, e.g. el...")
 
 
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'''[[File:vasp_logo.png|349x192px|alt=Vasp|none]]'''
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'''[[File:vasp_logo.png|none|alt=Vasp|349x192px]]'''
  
  
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VASP is a complex package for performing ab-initio quantum-mechanical molecular dynamics (MD) simulations using pseudopotentials or the projector-augmentedwave method and a plane wave basis set. The approach implemented in VASP is based on the (finite-temperature)local-density approximation with the free energy as variational quantity andan exact evaluation of the instantaneous electronic ground state at each MD time step. VASP uses efficient matrix diagonalisation schemesand an efficient Pulay/Broyden charge density mixing.These techniques avoid all problems possibly occurring in the original Car-Parrinello method,which is based on the simultaneous integration of electronic and ionicequations of motion.The interaction between ions and electrons is described by ultra-softVanderbilt pseudopotentials (US-PP) or by the projector-augmentedwave (PAW) method.US-PP (and the PAW method) allow for a considerablereduction of the number of plane-waves per atom fortransition metals and first row elements.Forces and the full stress tensor can be calculated with VASP and used to relaxatoms into their instantaneous ground-state.
 
VASP is a complex package for performing ab-initio quantum-mechanical molecular dynamics (MD) simulations using pseudopotentials or the projector-augmentedwave method and a plane wave basis set. The approach implemented in VASP is based on the (finite-temperature)local-density approximation with the free energy as variational quantity andan exact evaluation of the instantaneous electronic ground state at each MD time step. VASP uses efficient matrix diagonalisation schemesand an efficient Pulay/Broyden charge density mixing.These techniques avoid all problems possibly occurring in the original Car-Parrinello method,which is based on the simultaneous integration of electronic and ionicequations of motion.The interaction between ions and electrons is described by ultra-softVanderbilt pseudopotentials (US-PP) or by the projector-augmentedwave (PAW) method.US-PP (and the PAW method) allow for a considerablereduction of the number of plane-waves per atom fortransition metals and first row elements.Forces and the full stress tensor can be calculated with VASP and used to relaxatoms into their instantaneous ground-state.
  
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'''Vasp Manual<br />'''
  
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'''Environment Variables. '''
 
  
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[[File:Vasp Manual.pdf|Vasp_Manual.pdf]]
  
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Your old bashrc is available from the old backup and contained Environment variable setting relevant to the old cluster.
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'''Environment Variables required for running VASP on Magus.  '''
  
  
 
The following lines need to be added to you .bashrc file for the new cluster.
 
The following lines need to be added to you .bashrc file for the new cluster.
  
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source /snufs/intel/composer_xe_2015.2.164/bin/compilervars.sh intel64
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source /snufs/intel/composer_xe_2015.2.164/bin/compilervars.sh intel64
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source /snufs/intel/impi/5.0.3.048/intel64/bin/mpivars.sh
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source /snufs/intel/impi/5.0.3.048/intel64/bin/mpivars.sh
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'''Location of VASP-5.3.5 Binaries on Magus '''
 
'''Location of VASP-5.3.5 Binaries on Magus '''
  
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/snufs/apps/vasp/5.3.5/intelmpi/
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/snufs/apps/vasp/5.3.5/intelmpi/
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'''Vasp for Hashwell '''
 
'''Vasp for Hashwell '''
  
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/snufs/apps/vasp/5.3.5/intelmpi/vasp.hw
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/snufs/apps/vasp/5.3.5/intelmpi/vasp.hw
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/snufs/apps/vasp/5.3.5/intelmpi/vasp.hw.gamma
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/snufs/apps/vasp/5.3.5/intelmpi/vasp.hw.gamma
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/snufs/apps/vasp/5.3.5/intelmpi/vasp.hw.nc
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/snufs/apps/vasp/5.3.5/intelmpi/vasp.hw.nc
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'''Vasp binaries for Sandybridge '''
 
'''Vasp binaries for Sandybridge '''
  
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/snufs/apps/vasp/5.3.5/intelmpi/vasp.sdb
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/snufs/apps/vasp/5.3.5/intelmpi/vasp.sdb
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/snufs/apps/vasp/5.3.5/intelmpi/vasp.sdb.gamma
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/snufs/apps/vasp/5.3.5/intelmpi/vasp.sdb.gamma
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/snufs/apps/vasp/5.3.5/intelmpi/vasp.sdb.nc
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/snufs/apps/vasp/5.3.5/intelmpi/vasp.sdb.nc
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'''List of Queues'''
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Current configuration is as below we can optimize more later.
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* serial_short ( 1 Core, Sandybridge
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* serial_long ( 1 Core ) , Sandybridge
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* short_sdb ( 4 to 8 ) High Priority, Sandybridge
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* med_sdb ( 8 to 64 ) High Priority , Sandybridge
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* high_mem ( 16 to 128 ) High Priority, Hashwell High Memory
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* med_hsw ( 8 to 64) High Priority , Hashwell
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* gpu ( 16 to 16 )
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* long_sdb ( 8 t0 128) Low priority, Premptable, SandyBridge
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* long_high_mem ( 8 to 128) Low priority, Premptable , Hashwell High Memory
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* long_hsw ( 8 to 128) Low priority, Premptable, Hashwell
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'''Job Submission script'''
 
'''Job Submission script'''
  
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Example can be copied from /snufs/apps/vasp/5.3.5/intelmpi/submit.lsf.example
  
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Example can be copied from /snufs/apps/vasp/5.3.5/intelmpi/submit.lsf.example
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'''Explanation is given below in braces. '''
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'''Explanation is given below in Blue. '''
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#!/bin/bash
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#BSUB -J Vaspp_benchnew <span style="color: #00ccff;">(Name of Job )</span>
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#BSUB -n 64 <span style="color: #00ccff;">( Number of cores requested from Scheduler )</span>
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#BSUB -q high_mem <span style="color: #00ccff;">( Name of the queue )</span>
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#BSUB -e error.%J <span style="color: #00ccff;">( Error File will in the name of error.JOBID )</span>
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#BSUB -o out.%J <span style="color: #00ccff;">( Output file will be in name of out.JOBID)</span>
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#BSUB -R "span[ptile=16]"
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MPI=64 <span style="color: #00ccff;">( Number of cores to submit Job on )</span>
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PPN=16 <span style="color: #00ccff;">( Processor tasks per node )</span>
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MYDIR=$(pwd)
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EXE=/snufs/apps/vasp/5.3.5/intelmpi/vasp.hw <span style="color: #00ccff;">( Executable path choose as per the processor architecture)</span>
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export I_MPI_DAPL_PROVIDER=ofa-v2-mlx4_0-1
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export I_MPI_FABRICS=shm:dapl
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export I_MPI_FALLBACK=0
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export OMP_NUM_THREADS=1
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export FORT_BUFFERED=yes
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export I_MPI_PIN_PROCESSOR_LIST=0-15
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rm -f host.list
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cat $LSB_DJOB_HOSTFILE > ./host.list
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env > log.env
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mpiexec.hydra -np $MPI -f ./host.list -genvall -ppn $PPN  $EXE > $MYDIR/vasp.out  2>&1
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#!/bin/bash
 +
#BSUB -J Vaspp_benchnew ( Name of Job )
 +
#BSUB -n 64 ( Number of cores requested from Scheduler )
 +
#BSUB -q high_mem ( Name of the queue )
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#BSUB -e error.%J ( Error File will in the name of error.JOBID )
 +
#BSUB -o out.%J ( Output file will be in name of out.JOBID)
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#BSUB -R "span[ptile=16]"
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<br />MPI=64 ( Number of cores to submit Job on )
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PPN=16 ( Processor tasks per node )
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MYDIR=$(pwd)
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EXE=/snufs/apps/vasp/5.3.5/intelmpi/vasp.hw ( Executable path choose as per the processor architecture) <br /><br /># Do not Change anything below this line
 +
export I_MPI_DAPL_PROVIDER=ofa-v2-mlx4_0-1
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export I_MPI_FABRICS=shm:dapl
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export I_MPI_FALLBACK=0
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export OMP_NUM_THREADS=1
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export FORT_BUFFERED=yes
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export I_MPI_PIN_PROCESSOR_LIST=0-15
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rm -f host.list
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cat $LSB_DJOB_HOSTFILE > ./host.list
 +
env > log.env
 +
mpiexec.hydra -np $MPI -f ./host.list -genvall -ppn $PPN  $EXE > $MYDIR/vasp.out  2>&1

Latest revision as of 01:04, 8 August 2015

Vasp


The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, from first principles.

VASP computes an approximate solution to the many-body Schrödinger equation, either within density functional theory (DFT), solving the Kohn-Sham equations, or within the Hartree-Fock (HF) approximation, solving the Roothaan equations. Hybrid functionals that mix the Hartree-Fock approach with density functional theory are implemented as well. Furthermore, Green's functions methods (GW quasiparticles, and ACFDT-RPA) and many-body perturbation theory (2nd-order Møller-Plesset) are available in VASP.

In VASP, central quantities, like the one-electron orbitals, the electronic charge density, and the local potential are expressed in plane wave basis sets. The interactions between the electrons and ions are described using norm-conserving or ultrasoft pseudopotentials, or the projector-augmented-wave method.

To determine the electronic groundstate, VASP makes use of efficient iterative matrix diagonalisation techniques, like the residual minimisation method with direct inversion of the iterative subspace (RMM-DIIS) or blocked Davidson algorithms. These are coupled to highly efficient Broyden and Pulay density mixing schemes to speed up the self-consistency cycle.

Introduction

VASP is a complex package for performing ab-initio quantum-mechanical molecular dynamics (MD) simulations using pseudopotentials or the projector-augmentedwave method and a plane wave basis set. The approach implemented in VASP is based on the (finite-temperature)local-density approximation with the free energy as variational quantity andan exact evaluation of the instantaneous electronic ground state at each MD time step. VASP uses efficient matrix diagonalisation schemesand an efficient Pulay/Broyden charge density mixing.These techniques avoid all problems possibly occurring in the original Car-Parrinello method,which is based on the simultaneous integration of electronic and ionicequations of motion.The interaction between ions and electrons is described by ultra-softVanderbilt pseudopotentials (US-PP) or by the projector-augmentedwave (PAW) method.US-PP (and the PAW method) allow for a considerablereduction of the number of plane-waves per atom fortransition metals and first row elements.Forces and the full stress tensor can be calculated with VASP and used to relaxatoms into their instantaneous ground-state.

Vasp Manual


File:Vasp Manual.pdf


Environment Variables required for running VASP on Magus. 


The following lines need to be added to you .bashrc file for the new cluster. 

source /snufs/intel/composer_xe_2015.2.164/bin/compilervars.sh intel64
source /snufs/intel/impi/5.0.3.048/intel64/bin/mpivars.sh

Location of VASP-5.3.5 Binaries on Magus 

/snufs/apps/vasp/5.3.5/intelmpi/

Vasp for Hashwell 

/snufs/apps/vasp/5.3.5/intelmpi/vasp.hw
/snufs/apps/vasp/5.3.5/intelmpi/vasp.hw.gamma
/snufs/apps/vasp/5.3.5/intelmpi/vasp.hw.nc

Vasp binaries for Sandybridge 

/snufs/apps/vasp/5.3.5/intelmpi/vasp.sdb
/snufs/apps/vasp/5.3.5/intelmpi/vasp.sdb.gamma
/snufs/apps/vasp/5.3.5/intelmpi/vasp.sdb.nc

Job Submission script 

Example can be copied from /snufs/apps/vasp/5.3.5/intelmpi/submit.lsf.example

Explanation is given below in braces. 

#!/bin/bash
#BSUB -J Vaspp_benchnew ( Name of Job )
#BSUB -n 64 ( Number of cores requested from Scheduler )
#BSUB -q high_mem ( Name of the queue )
#BSUB -e error.%J ( Error File will in the name of error.JOBID )
#BSUB -o out.%J ( Output file will be in name of out.JOBID)
#BSUB -R "span[ptile=16]"

MPI=64 ( Number of cores to submit Job on )
PPN=16 ( Processor tasks per node )
MYDIR=$(pwd)
EXE=/snufs/apps/vasp/5.3.5/intelmpi/vasp.hw ( Executable path choose as per the processor architecture) 

# Do not Change anything below this line
export I_MPI_DAPL_PROVIDER=ofa-v2-mlx4_0-1
export I_MPI_FABRICS=shm:dapl
export I_MPI_FALLBACK=0
export OMP_NUM_THREADS=1
export FORT_BUFFERED=yes
export I_MPI_PIN_PROCESSOR_LIST=0-15
rm -f host.list
cat $LSB_DJOB_HOSTFILE > ./host.list
env > log.env 
mpiexec.hydra -np $MPI -f ./host.list -genvall -ppn $PPN  $EXE > $MYDIR/vasp.out  2>&1
Retrieved from "https://wiki.snu.edu.in/index.php?title=HPC_VASP&oldid=33"
Author
Deepak Agrawal