Submitting Jobs

Quick Description: "The Vienna Ab-initio Simulation Package, better known as VASP, is a package for performing ab initio quantum mechanical molecular dynamics (MD) using either Vanderbilt pseudopotentials, or the projector augmented wave method, and a plane wave basis set. The basic methodology is density functional theory (DFT), but the code also allows use of post-DFT corrections such as hybrid functionals mixing DFT and Hartree-Fock exchange, many-body perturbation theory (the GW method) and dynamical electronic correlations within the random phase approximation." -- wikipedia

The Point: You give VASP atomic coordinates (POSCAR), job specifications (INCAR and KPOINTS), and a library of information on the atoms used (POTCAR), and it will spit back out for you an optimized system (CONTCAR, OSZICAR, etc...). (You may need vdw_kernel.bindat for jobs requiring van der Waals)

Prerequisites: Probably you may want to use some older jobs as reference for building your newer jobs, or use something like VESTA, or Gaussview, to get a loose structure built for your jobs.

Notes:

1. Open WinSCP and navigate to the folder containing the necessary items for running a job

• POSCAR
• POTCAR
• INCAR
• KPOINTS
• (vdw_kernel.bindat)

1. Drag this folder over to your own folder on the group server: "bartels/sharedData/<your name>"
2. Launch putty (or whatever) to ssh into the group server and again navigate to the folder containing your job (using "cd <directory>")
3. "qsub ~/g8vasp" (for example for a normal job)

Sometimes you may want to pick a certain node to submit to. Generally, qsub queues your job so that it waits in line for the next available computer that meets your core specifications. Say, however, you need a larger amount of memory to accommodate your job. In my case, I needed a high core and high memory computer. Looking at what was available to me on our group server, I found that vasp3 and vasp12 met my requirements.

So I submitted using: "qsub -l nodes=vasp12:ppn=24 ~/g24vasp"

This can be broke down into 3 parts that you would actually change: "vasp12", "ppn=24", and "~/g24vasp". Basically, you need to pick which computer you want, specify the number of cores it has, and use the submission script associated with the type of job you wish to run.

Additionally, there is another script for access to more RAM: "g2vasp_x3". This script runs three 2-core machines in parallel, effectively producing a 6-core machine with 31G of RAM.o I submitted using: "qsub -l nodes=vasp12:ppn=24 ~/g24vasp"