VASP

VASP is a package for performing ab initio quantum-mechanical molecular dynamics (MD) using pseudopotentials and a plane wave basis set. The approach implemented in VASP is based on a finite-temperature local-density approximation (with the free energy as variational quantity) and an exact evaluation of the instantaneous electronic ground state at each MD step using efficient matrix diagonalization schemes and an efficient Pulay mixing.

Access

VASP is available only to NERSC users who already have an existing VASP license. If you have a VASP license, send your license information to the VASP support at Vienna at vasp.materialphysik@univie.ac.at (and copy vasp_licensing@nersc.gov) requesting that they confirm your VASP license to NERSC staff at vasp_licensing@nersc.gov in order to gain access to the VASP binaries at NERSC.

Note

NERSC does not provide the VASP 4 modules anymore.

It may take several business days from the date when your confirmation request is sent to the VASP support at Vienna to you actually gain the access to the VASP binaries provided at NERSC. If the confirmation takes longer than 5 business days, update the initial email thread with the license information.

When your VASP license is confirmed, NERSC will add you to a unix file group: vasp5 for VASP 5. You can check if you have the VASP access at NERSC or not by typing the groups command. If you are in the vasp5 file group, then you can access VASP 5 binaries provided at NERSC.

Modules

We provide multiple VASP builds for users. To see what VASP modules are available:

cori$ module avail vasp
For example, these are the available modules (as of 7/8/2019),

cori$ module avail vasp

------------------------- /usr/common/software/modulefiles --------------------------
vasp/5.4.1-hsw                    vasp/20170629-hsw      vasp-tpc/5.4.1-hsw
vasp/5.4.1-knl                    vasp/20170629-knl      vasp-tpc/5.4.1-knl
vasp/5.4.4-hsw(default)           vasp/20171017-hsw      vasp-tpc/5.4.4-hsw(default)
vasp/5.4.4-knl                    vasp/20171017-knl      vasp-tpc/5.4.4-knl
vasp/20170323_NMAX_DEG=128-hsw    vasp/20181030-hsw      vasp-tpc/20170629-hsw
vasp/20170323_NMAX_DEG=128-knl    vasp/20181030-knl      vasp-tpc/20170629-knl

Where the modules with "5.4.4" or "5.4.1" in their version strings are the builds of the pure MPI VASP codes, and the modules with "2018" or "2017" in their version strings are the builds of the hybrid MPI+OpenMP VASP codes. The vasp-tpc (tpc stands for third party codes) modules are the custom builds incorporating commonly used third party contributed codes, e.g., the VTST code from University of Texas at Austin, Wannier90, BEFF, VASPSol, etc.. The "knl" and "hsw" in the version strings indicate the modules are optimal builds for Cori KNL and Haswell, respectively. The current default on Cori is vasp/5.4.4-hsw (release date: April 17, 2017, with the latest patches). and you can access it by

cori$ module load vasp
To use other non-default module, you need to provide the full module name,
cori$ module load vasp/20181030-knl
The "module show" command shows what VASP modules do to your environment, e.g.

cori$ module show vasp/20181030-knl
-------------------------------------------------------------------
/usr/common/software/modulefiles/vasp/20181030-knl:

module       load craype-hugepages2M 
module-whatis    VASP: Vienna Ab-initio Simulation Package
This is the vasp-knl development version (last commit 10/30/2018). Wannier90 v1.2 was enabled in the build.

setenv       PSEUDOPOTENTIAL_DIR /usr/common/software/vasp/pseudopotentials/5.3.5 
setenv       VDW_KERNAL_DIR /usr/common/software/vasp/vdw_kernal 
setenv       NO_STOP_MESSAGE 1 
setenv       MPICH_NO_BUFFER_ALIAS_CHECK 1 
setenv       MKL_FAST_MEMORY_LIMIT 0 
setenv       OMP_STACKSIZE 256m 
setenv       OMP_PROC_BIND spread 
setenv       OMP_PLACES threads 
prepend-path     PATH /usr/common/software/vasp/vtstscripts/3.1
prepend-path     PATH /global/common/cori/software/vasp/20181030/knl/intel/bin 
-------------------------------------------------------------------

This vasp module adds the path to the VASP binaries to your search path, and also sets a few environment variables. Where PSEUDOPOTENTIAL_DIR and VDW_KERNAL_DIR are defined for the locations of the pseudopotential files and the vdw_kernel.bindat file used in dispersion calculations. The OpenMP and MKL environment variables are set for optimal performance.

Vasp binaries

Each VASP module provides the three different binaries:

  • vasp_gam - gamma point only build
  • vasp_ncl - non-collinear spin
  • vasp_std - the standard kpoint binary

You need to choose an appropriate binary to run your job.

Running batch jobs

To run batch jobs, you need to prepare a job script (see samples below), and submit it to the batch system with the "sbatch" command. Assume the job script is named as run.slurm,

cori$ sbatch run.slurm

Please check the Queue Policy page for the available QOS's and their resource limits.

Cori Haswell

  1. A sample job script to run the Pure MPI VASP codes
#!/bin/bash
#SBATCH -N 1
#SBATCH -C haswell
#SBATCH -q regular
#SBATCH -t 6:00:00

module load vasp
srun -n32 -c2 --cpu_bind=cores vasp_std
  1. A sample job script to run the hybrid MPI+OpenMP VASP codes
#!/bin/bash
#SBATCH -N 2 
#SBATCH -C haswell
#SBATCH -q regular
#SBATCH -t 6:00:00

module load vasp/20181030-hsw
export OMP_NUM_THREADS=4

# launching 1 task every 4 cores (8 CPUs)
srun -n16 -c8 --cpu_bind=cores vasp_std

Cori KNL

  1. A sample job scripts to run the Pure MPI VASP codes
#!/bin/bash
#SBATCH -N 2 
#SBATCH -C knl
#SBATCH -q regular
#SBATCH -t 6:00:00

module load vasp/5.4.4-knl
srun -n128 -c4 --cpu_bind=cores vasp_std
  1. A sample job scripts to run the hybrid MPI+OpenMP VASP codes
#!/bin/bash
#SBATCH -N 2 
#SBATCH -C knl
#SBATCH -q regular
#SBATCH -t 6:00:00

module load vasp/20181030-knl
export OMP_NUM_THREADS=4

# launching 1 task every 4 cores (16 CPUs)
srun -n32 -c16 --cpu_bind=cores vasp_std

Tips

  1. For a better job throughput, run jobs on Cori KNL.
  2. The hybrid MPI+OpenMP VASP are recommended on Cori KNL for optimal performance.
  3. More performance tips can be found in a Cray User Group 2017 proceeding
  4. Also refer to the presentation slides for the VASP user training (6/18/2019).

Runninge interactively

To run VASP interactively, you need to request a batch session using the "salloc" command, e.g., the following command requests one Cori Haswell node for one hour,

cori$ salloc -N 1 -q interactive -C haswell -t 1:00:00

When the batch session returns with a shell prompt, execute the following commands:

cori$ module load vasp 
cori$ srun -n32 -c2 --cpu-bind=cores vasp_std
To run on Cori KNL interactively, do

cori$ salloc -N 2 -q interactive -C knl -t 4:00:00

The above command requests two KNL nodes for four hours. When the batch session returns with a shell prompt, execute the following commands:

cori$ module load vasp/20181030-knl
cori$ export OMP_NUM_TRHEADS=4
cori$ srun -n32 -c16 --cpu-bind=cores vasp_std

Tips

  1. The interactive QOS allocates the requested nodes immediately or cancels your job in about 5 minutes (when no nodes are available). See the Queue Policy page for more info.
  2. Test your job using the interactive QOS before submitting a long running job.

VASP makefiles

If you need to build VASP by yourselves, use the makefiles available at the VASP installation directories. For example, the "makefile.include" file that we used to build the vasp/5.4.4-hsw module is available at,

/global/common/sw/cray/cnl6/haswell/vasp/5.4.4/intel/17.0.2.174/4bqi2il 

Type module show`` to find the installation directory.

Documentation

VASP Online Manual