VASP

VASP

VASP [1] is a complex ab-initio quantum-mechanical molecular dynamics (MD) simulations package.

Important Notes

• VASP is licensed to a vasp group. Al Anderson, Dan Lacks, and Arthur Heuer must authorize “vasp” group privileges for any users on the cluster. 

• If you are interested in using VASP, please get permission from vasp group and contact HPC support.

• Create different sub-directories for different jobs so as not to copy huge data back and froth.

Installed Versions

All the available versions of VASP for use can be viewed by issuing the following command. This applies for other applications as well.

module spider vasp 

output:

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vasp: vasp/5.4.4

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Description:

VASP (VASP is a complex ab-initio quantum-mechanical molecular dynamics (MD) simulations package.

You will need to load all module(s) on any one of the lines below before the "vasp/5.4.4" module is available to load.

gcc/6.3.0 openmpi/2.0.1

The default version can be loaded as:

module load vasp

Running VASP

Copy the directory “silica_work” from /usr/local/doc/VASP/silica_work to your home directory and go to silica_work directory.

cp -r /usr/local/doc/VASP/silica_work .

cd silica_work

You will also find pbs script file “job” in that directory along with other input files.

Parallel Job

Make sure that NPAR = #processors (nodes*ppn) in INCAR file. For example, if you you using NPAR=4, one option is to modify the #SBATCH line in a job file as:

#SBATCH -N 2 -n 4 # 2 nodes and 4 processors

Submit the job:

sbatch job.slurm

Excerpt from "OUTCAR" outputfile. Note the speedup using 4 processors.

vasp.5.4.4.18Apr17-6-g9f103f2a35 (build May 24 2019 10:39:41) complex           

 executed on             LinuxGNU date 2019.06.03  11:15:36

 running on    4 total cores

 distrk:  each k-point on    4 cores,    1 groups

 distr:  one band on NCORES_PER_BAND=   1 cores,    4 groups

...

General timing and accounting informations for this job:

 ========================================================

                  Total CPU time used (sec):      117.896

                            User time (sec):      104.797

                          System time (sec):       13.099

                         Elapsed time (sec):      131.151

                   Maximum memory used (kb):       90468.

                   Average memory used (kb):           0.

                          Minor page faults:       436907

                          Major page faults:            3

                 Voluntary context switches:        10165

Parallel job may require more than 1gb memory and may go through many iterations. So, request the walltime appropriately. Also, follow references for parallel implementations.

Analyze and Visualize

To analyze and visualize the output, visit HPC Guide to VaspTools.

Learning & Performance

The VASP Wiki is a useful reference for developing insight into the computational framework. Follow links to the manual, getting start, and then lectures, and/or tutorials and examples. Lecture notes concerning use of VASP on HPC may be of particular interest.

References:

[1] VASP Home: http://cms.mpi.univie.ac.at/vasp/vasp/vasp.html

[2] For more examples, copy the VASP-examples.tar at /usr/local/src/vasp/ obtained from workshop http://www.nsc.liu.se/lcsc2005/tutor.html .

[3] http://www.cuhk.edu.hk/itsc/compenv/research-computing/organon/vasp.html